Nothing
R/GeneralMethodComet.R
In coMET: coMET: visualisation of regional epigenome-wide association scan (EWAS) results and DNA co-methylation patterns
Defines functions
create.tracks.web
create.tracks.user
draw.name.tracks.web
draw.name.genes.web
create.symbol.list.large
create.symbol.list
create.color.list.large
create.color.list
create.color.bar
draw.plot.grid.mydata.names
draw.legend
draw.plot.cormatrix.plot
draw.plot.grid.mydata.large
draw.plot.grid.mydata
draw.plot.mydata.ggbio
draw.plot.annotation
draw.plot.axis.data
draw.plot.linesconnection
draw.plot.grid.setup
Documented in
create.color.bar
create.color.list
create.color.list.large
create.symbol.list
create.symbol.list.large
create.tracks.user
create.tracks.web
draw.legend
draw.name.genes.web
draw.name.tracks.web
draw.plot.annotation
draw.plot.axis.data
draw.plot.cormatrix.plot
draw.plot.grid.mydata
draw.plot.grid.mydata.large
draw.plot.grid.mydata.names
draw.plot.grid.setup
draw.plot.linesconnection
draw.plot.mydata.ggbio
##########################################################################
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
##########################################################################
##########################################################################
# File: GeneralMethodComet.R
# Author: Tiphaine Martin
# Email: tiphaine.martin@kcl.ac.uk
# Purpose: coMET allows the display of p-values from association
# with a correlation heatmap.
# Version : 0.99.9
###########################################################################
#-------------------DRAW PLOT GRID----------------------------
draw.plot.grid.setup <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.GRID.SETUP\n")
#set y-axis initial value
if(config.var$disp.pval.threshold != -1) {
gbl.var$r.y[1] <- config.var$disp.pval.threshold
gbl.var$axis.y <- seq(floor(gbl.var$r.y[1]), max(gbl.var$axis.y))
} else {
gbl.var$r.y[1] <- 0
}
#-------------------VIEWPORT BEGINS------------------
#-------------------CORMATRIX VIEWPORT---------------------
# FOR CORMATRIX MAP
top.vp.cormatrixmap <- viewport(layout = grid.layout(7, 3, widths = c(0.18, 0.6875, 0.1325),
heights = c(.05, .025, .18, .24, .001, .5, .05)),
name = "top.vp.cormatrixmap")
top.vp.nocormatrixmap <- viewport(layout = grid.layout(6, 3, widths = c(0.18, 0.6875, 0.1325),,
heights = c(.05, .025, .42, .001, .5, .05)),
name = "top.vp.nocormatrixmap")
top.vp.cormatrixmap.nopval <- viewport(layout = grid.layout(6, 3, widths = c(0.18, 0.6875, 0.1325),
heights = c(.05, .025, .42, .001, .5, .05)),
name = "top.vp.cormatrixmap.nopval")
if(config.var$disp.pvalueplot){
if(config.var$disp.cormatrixmap) {
gbl.var$top.vp <- top.vp.cormatrixmap
}
else {
gbl.var$top.vp <- top.vp.nocormatrixmap
}
} else {
gbl.var$top.vp <- top.vp.cormatrixmap.nopval
}
#-------------------TITLE VIEWPORT---------------------
title.vp.cormatrixmap <- viewport(height = .8,
width = .8,
layout.pos.row = 1,
layout.pos.col = 2,
name = "title.vp.cormatrixmap")
title.vp.nocormatrixmap <- viewport(height = .8,
width = .8,
layout.pos.row = 1,
layout.pos.col = 2,
name = "title.vp.nocormatrixmap")
title.vp.cormatrixmap.nopval <- viewport(height = .8,
width = .8,
layout.pos.row = 1,
layout.pos.col = 2,
name = "title.vp.cormatrixmap.nopval")
if(config.var$disp.pvalueplot){
if(config.var$disp.cormatrixmap) {
pushViewport(vpTree(top.vp.cormatrixmap, vpList(title.vp.cormatrixmap )))
}
else {
pushViewport(vpTree(top.vp.nocormatrixmap, vpList(title.vp.nocormatrixmap )))
}
}else{
pushViewport(vpTree(top.vp.cormatrixmap.nopval, vpList(title.vp.cormatrixmap.nopval)))
}
image.title.text <- textGrob(config.var$image.title, x = 0.5, y = 0.5, just = c("center"),
default.units = "native", gp = gpar(fontsize = (gbl.var$font.size + 4 *config.var$font.factor), fontface = "bold.italic"))
image.title <- gTree(children=gList(image.title.text), vp=title.vp.cormatrixmap, name="image.title")
grid.draw(image.title)
#--------------------- PLOT CHROMOSOME ------------------------
popViewport()
chromosome.vp.cormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 2,
layout.pos.col = 2,
name = "chromosome.vp.cormatrixmap")
chromosome.vp.nocormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 2,
layout.pos.col = 2,
name = "chromosome.vp.nocormatrixmap")
chromosome.vp.cormatrixmap.nopval <- viewport(height = 1,
width = 1,
layout.pos.row = 2,
layout.pos.col = 2,
name = "chromosome.vp.cormatrixmap.nopval")
if(config.var$disp.pvalueplot){
if(config.var$disp.cormatrixmap) {
pushViewport(vpTree(top.vp.cormatrixmap, vpList(chromosome.vp.cormatrixmap )))
}
else {
pushViewport(vpTree(top.vp.nocormatrixmap, vpList(chromosome.vp.nocormatrixmap )))
}
} else {
pushViewport(vpTree(top.vp.cormatrixmap.nopval, vpList(chromosome.vp.cormatrixmap.nopval )))
}
itrack <- IdeogramTrack(genome=gbl.var$mydata.gen, chromosome=gbl.var$mydata.chr)
plotTracks(itrack,from=gbl.var$min.x,to=gbl.var$max.x,panel.only=TRUE, fontsize=config.var$fontsize.gviz,showBandId = TRUE, cex.bands = 0.5)
#-------------------CONNECTOR VIEWPORT---------------------
if(config.var$disp.cormatrixmap) {
if(config.var$disp.pvalueplot){
draw.plot.linesconnection(top.vp.cormatrixmap, config.var, gbl.var)
} else {
draw.plot.linesconnection(top.vp.cormatrixmap.nopval, config.var, gbl.var)
}
}
else {
popViewport()
}
#-------------------DATA VIEWPORT---------------------
if(config.var$disp.cormatrixmap & config.var$disp.pvalueplot) {
draw.plot.axis.data(top.vp.cormatrixmap, config.var, gbl.var)
}
else {
if(config.var$disp.cormatrixmap==FALSE & config.var$disp.pvalueplot){
draw.plot.axis.data(top.vp.nocormatrixmap, config.var, gbl.var)
} else {
popViewport()
}
}
#--------------------- POSITION of LEGEND PHYSICAL DISTANCE ------------------------
#display the physical distance on plots without LD maps
if(config.var$disp.phys.dist & !config.var$disp.cormatrixmap) {
if(gbl.var$total.dist > 1000) {
grid.text(paste("Physical Distance: ", round(gbl.var$total.dist/1000, 1), " kb", sep=""),
x = 0.5,
y = -1.15,
just = "center",
gp = gpar(fontsize = (gbl.var$font.size*config.var$font.factor)))
} else {
grid.text(paste("Physical Distance: ",
gbl.var$total.dist, " bases", sep=""),
x = 0.5, y = -1.15,
just = "center",
gp = gpar(fontsize = (gbl.var$font.size*config.var$font.factor)))
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.GRID.SETUP\n")
return(gbl.var)
}
#------------------- DRAW CONNECTOR -----------------------
draw.plot.linesconnection <- function(top.vp, config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.LINESCONNECTION\n")
popViewport()
# if (config.var$verbose) cat("gbl.var$r.x[1]", gbl.var$r.x[1], "\n")
# if (config.var$verbose) cat("gbl.var$r.y[2]", gbl.var$r.y[2], "\n")
# if (config.var$verbose) cat("gbl.var$axis.x[length(gbl.var$axis.x)]", gbl.var$axis.x[length(gbl.var$axis.x)], "\n")
# if (config.var$verbose) cat("gbl.var$axis.y[1]", gbl.var$axis.y[1], "\n")
#-------------------CONNECTOR VIEWPORT---------------------
connector.vp.cormatrixmap <- viewport(xscale = c(gbl.var$r.x[1], gbl.var$axis.x[length(gbl.var$axis.x)]),
yscale = c(gbl.var$axis.y[1], gbl.var$r.y[2]),
height = 0.8,
width = 0.8,
layout.pos.row = 5,
layout.pos.col = 2,
name = "data.vp.cormatrixmap")
connector.vp.cormatrixmap.nopval <- viewport(xscale = c(gbl.var$r.x[1], gbl.var$axis.x[length(gbl.var$axis.x)]),
yscale = c(gbl.var$axis.y[1], gbl.var$r.y[2]),
height = 0.8,
width = 0.8,
layout.pos.row = 4,
layout.pos.col = 2,
name = "data.vp.cormatrixmap.nopval")
if(config.var$disp.cormatrixmap) {
if(config.var$disp.pvalueplot) {
pushViewport(vpTree(top.vp, vpList(connector.vp.cormatrixmap)))
} else{
pushViewport(vpTree(top.vp, vpList(connector.vp.cormatrixmap.nopval)))
}
}
#-------------------AXIS BEGINS------------------
# if (config.var$verbose) cat("axis\n")
grid.lines(x = gbl.var$axis.x, y = 0, default.units = "native", gp = gpar(lty = 1, lwd = gbl.var$line.width))
#----------------------- X-AXIS --------------------------
# if (config.var$verbose) cat("x-axis\n")
if(config.var$disp.mult.lab.X) {
#Truncate the number of X-axis labels
if(length(gbl.var$axis.x) > 5) {
increment <- ceiling(length(gbl.var$axis.x) / 5)
axis.x.labels <- gbl.var$axis.x[seq(1, length(gbl.var$axis.x), by= increment)]
if(length(gbl.var$axis.x) %% 5 != 0) {
axis.x.labels <- c(axis.x.labels, gbl.var$axis.x[length(gbl.var$axis.x)])
}
}
}
else {
#Truncate the number of X-axis labels
if(length(gbl.var$axis.x) >= 2) {
axis.x.labels <- c(head(gbl.var$axis.x, 1), tail(gbl.var$axis.x, 1))
}
}
#DEBUG STATEMENT
# if (config.var$verbose) cat("cormatrixmap\n")
# if (config.var$verbose) cat("List",gbl.var$sorted.mydata.pos,"\n")
# if (config.var$verbose) cat("gbl.var$sorted.mydata.pos.zoom ", gbl.var$sorted.mydata.pos.zoom, "\n")
# if (config.var$verbose) cat("List zoom",gbl.var$sorted.mydata.pos.zoom,"\n")
grid.xaxis(at = axis.x.labels, label = FALSE, gp = gpar(cex = gbl.var$cex.factor), name = "axis.x.labels")
grid.xaxis(at = gbl.var$sorted.mydata.pos.zoom, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width))
grid.text(paste(axis.x.labels[1],"bp"), x = -0.025, y = -0.1, just = "right", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
grid.text(paste(axis.x.labels[2],"bp"), x = 1.015, y = -0.1, just = "left", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
if(config.var$disp.color.ref) {
#Color darkorchid1 the reference
grid.xaxis(at = gbl.var$mydata.ref.pos, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width,col="darkorchid1"))
}
#Remove trailing tick mark
grid.edit("axis.x.labels", gp = gpar(col = "white"))
#------------------ X-AXIS -----------------------
#-------------------EQUIDISPOS COORDINATE BEGINS-------------
# if (config.var$verbose) cat("equidistance\n")
gbl.var$equidis.pos <- NULL
#DEBUG STATEMENT
# if (config.var$verbose) cat("length(gbl.var$equidis.pos) ", length(gbl.var$equidis.pos), "\n")
# if (config.var$verbose) cat("length(gbl.var$mydata.num) ", length(gbl.var$mydata.pos), "\n")
gbl.var$mydata.num <- length(gbl.var$sorted.mydata.pos)
pos.increment <- (gbl.var$max.x - gbl.var$min.x) / gbl.var$mydata.num
#Attempt to center the MYDATA labels
start.pos <- gbl.var$min.x
for(i in 0:(gbl.var$mydata.num - 1)) {
gbl.var$equidis.pos <- c(gbl.var$equidis.pos, pos.increment * i + start.pos)
}
#-------------------CONNECTING LINES BEGINS-------------
if(config.var$connecting.lines.adj == -1) {
dev.off()
stop("connecting.lines.adj may not equal: -1")
}
tmp.correction.factor <- gbl.var$equidis.pos[1] * 10^(gbl.var$cur.exp - 9) * (1 + config.var$connecting.lines.adj)
#DEBUG STATEMENT
# if (config.var$verbose) cat("tmp.correction.factor ", tmp.correction.factor, "\n")
# if (config.var$verbose) cat("length(gbl.var$sorted.mydata.pos) ", length(gbl.var$sorted.mydata.pos), "\n")
# if (config.var$verbose) cat("length(gbl.var$equidis.pos) ", length(gbl.var$equidis.pos), "\n")
# if (config.var$verbose) cat("gbl.var$equidis.pos[1] ", gbl.var$equidis.pos[1], "\n")
# if (config.var$verbose) cat("gbl.var$cur.exp ", gbl.var$cur.exp, "\n")
# if (config.var$verbose) cat("config.var$connecting.lines.adj ", config.var$connecting.lines.adj, "\n")
length.sorted.mydata.pos.zoom <- length(gbl.var$sorted.mydata.pos.zoom)
if(config.var$image.size == 3.5) {
y.finish.pos <- rep(-0.9, length.sorted.mydata.pos.zoom * config.var$connecting.lines.factor)
} else if(config.var$image.size == 7) {
y.finish.pos <- rep(-1.8, length.sorted.mydata.pos.zoom * config.var$connecting.lines.factor)
}
#DEBUG STATEMENT
# if (config.var$verbose) cat("gbl.var$axis.y[1] ", gbl.var$axis.y[1], "\n")
# if (config.var$verbose) cat("y.finish.pos ", y.finish.pos, "\n")
if(config.var$connecting.lines.vert.adj != -1) {
y.start.pos <- config.var$connecting.lines.vert.adj
} else if (config.var$image.size == 3.5) {
y.start.pos <- -0.5
} else if (config.var$image.size == 7) {
y.start.pos <- -0.7
}else {
dev.off()
stop("Invalid image size: ", config.var$image.size, "\n")
}
# if (config.var$verbose) cat("BUG HERE \n")
# if (config.var$verbose) cat("BUGgg HERE \n")
x.finish.pos <- gbl.var$equidis.pos +
seq(1, length(gbl.var$equidis.pos) * abs(tmp.correction.factor), abs(tmp.correction.factor)) * config.var$connecting.lines.flex +
gbl.var$total.dist * config.var$connecting.lines.adj
#for reference sequence
ref.position <- which(gbl.var$sorted.mydata.pos == gbl.var$mydata.ref.pos)
x.finish.pos.zoom.ref <- x.finish.pos[ref.position]
#for region study
remove.position <- which(gbl.var$sorted.mydata.pos < gbl.var$min.x | gbl.var$sorted.mydata.pos > gbl.var$max.x)
if(length(remove.position) > 0){
x.finish.pos.zoom <- x.finish.pos[-remove.position]
} else {
x.finish.pos.zoom <- x.finish.pos
}
# if (config.var$verbose) cat("y.finish.pos ", y.finish.pos, "\n")
# if (config.var$verbose) cat("y.start.pos ", y.start.pos, "\n")
# if (config.var$verbose) cat("gbl.var$min.x ", gbl.var$min.x, "\n")
# if (config.var$verbose) cat("gbl.var$max.x ", gbl.var$max.x, "\n")
# if (config.var$verbose) cat("x.finish.pos", x.finish.pos, "\n")
# if (config.var$verbose) cat("remove.position", remove.position, "\n")
# if (config.var$verbose) cat("x.finish.pos.zoom ", x.finish.pos.zoom, "\n")
# if (config.var$verbose) cat("gbl.var$sorted.mydata.pos.zoom ", gbl.var$sorted.mydata.pos.zoom, "\n")
if(config.var$image.size == 3.5) {
connecting.lines <- segmentsGrob(x0 = x.finish.pos.zoom,
x1 = gbl.var$sorted.mydata.pos.zoom,
y0 = unit(y.finish.pos, "char"),
y1 = unit(y.start.pos, "char"),
default.units = "native",
gp = gpar(lwd = gbl.var$line.width))
######ref
if(config.var$disp.color.ref) {
######ref
if(gbl.var$mydata.ref.pos > gbl.var$min.x & gbl.var$mydata.ref.pos < gbl.var$max.x){
connecting.lines.ref <- segmentsGrob(x0 = x.finish.pos.zoom.ref,
x1 = gbl.var$mydata.ref.pos,
y0 = unit(y.finish.pos, "char"),
y1 = unit(y.start.pos,"char"),
default.units = "native",
gp = gpar(lwd = gbl.var$line.width,col="darkorchid1"))
}
}
} else if(config.var$image.size == 7) {
connecting.lines <- segmentsGrob(x0 = x.finish.pos.zoom,
x1 = gbl.var$sorted.mydata.pos.zoom,
y0 = unit(y.finish.pos, "char"),
y1 = unit(y.start.pos,"char"),
default.units = "native",
gp = gpar(lwd = gbl.var$line.width))
if(config.var$disp.color.ref) {
######ref
if(gbl.var$mydata.ref.pos > gbl.var$min.x & gbl.var$mydata.ref.pos < gbl.var$max.x){
connecting.lines.ref <- segmentsGrob(x0 = x.finish.pos.zoom.ref,
x1 = gbl.var$mydata.ref.pos,
y0 = unit(y.finish.pos, "char"),
y1 = unit(y.start.pos,"char"),
default.units = "native",
gp = gpar(lwd = gbl.var$line.width,col="darkorchid1"))
}
}
} else {
dev.off()
stop("Invalid image size: ", config.var$image.size, "\n")
}
# if (config.var$verbose) cat("BUGG HERE \n")
#DEBUG STATEMENT
# if (config.var$verbose) cat("y.finish.pos ", y.finish.pos, "\n")
# if (config.var$verbose) cat("connecting.lines ", is.null(connecting.lines), "\n")
# cat(is.null(connecting.lines), "\n")
# cat(x.finish.pos, "\n")
# cat(gbl.var$sorted.mydata.pos, "\n")
#----------------------- X-AXIS --------------------------
grid.lines(x = gbl.var$axis.x, y = 0, default.units = "native", gp = gpar(lty = 1, lwd = gbl.var$line.width, col="gray80"))
if(config.var$disp.connecting.lines) {
grid.draw(connecting.lines)
if(config.var$disp.color.ref) {
grid.draw(connecting.lines.ref)
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.LINECONNECTION\n")
}
#------------------- DRAW AXIS DATA -----------------------
draw.plot.axis.data <- function(top.vp, config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.AXIS.DATA\n")
popViewport()
#-------------------DATA VIEWPORT---------------------
data.vp.cormatrixmap <- viewport(xscale = c(gbl.var$r.x[1], gbl.var$axis.x[length(gbl.var$axis.x)]),
yscale = c(gbl.var$axis.y[1], gbl.var$r.y[2]),
height = 0.8,
width = 0.8,
layout.pos.row = 3,
layout.pos.col = 2,
name = "data.vp.cormatrixmap")
data.vp.nocormatrixmap <- viewport(xscale = c(gbl.var$r.x[1], gbl.var$axis.x[length(gbl.var$axis.x)]),
yscale = c(gbl.var$axis.y[1], gbl.var$r.y[2]),
height = .8,
width = .8,
layout.pos.row = 3,
layout.pos.col = 2,
name = "data.vp.nocormatrixmap")
if(config.var$disp.cormatrixmap) {
pushViewport(vpTree(top.vp, vpList(data.vp.cormatrixmap)))
}
else {
pushViewport(vpTree(top.vp, vpList(data.vp.nocormatrixmap)))
}
#-------------------AXIS BEGINS------------------
grid.lines(x = gbl.var$axis.x, y = gbl.var$axis.y[1], default.units = "native", gp = gpar(lty = "dashed", lwd = gbl.var$line.width))
#----------------------- X-AXIS --------------------------
if(config.var$disp.mult.lab.X) {
#Truncate the number of X-axis labels
if(length(gbl.var$axis.x) > 5) {
increment <- ceiling(length(gbl.var$axis.x) / 5)
axis.x.labels <- gbl.var$axis.x[seq(1, length(gbl.var$axis.x), by= increment)]
if(length(gbl.var$axis.x) %% 5 != 0) {
axis.x.labels <- c(axis.x.labels, gbl.var$axis.x[length(gbl.var$axis.x)])
}
}
}
else {
#Truncate the number of X-axis labels
if(length(gbl.var$axis.x) >= 2) {
axis.x.labels <- c(head(gbl.var$axis.x, 1), tail(gbl.var$axis.x, 1))
}
}
if(config.var$disp.cormatrixmap) {
if(! is.null(config.var$mydata.large.file)){
grid.xaxis(at = gbl.var$sorted.mydata.large.pos.zoom, label = FALSE, gp = gpar(col="grey", cex = gbl.var$cex.factor, lwd = gbl.var$line.width))
}
grid.xaxis(at = axis.x.labels, label = FALSE, gp = gpar(cex = gbl.var$cex.factor), name = "axis.x.labels")
grid.xaxis(at = gbl.var$sorted.mydata.pos.zoom, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width))
grid.text(paste(axis.x.labels[1],"bp"), x = -0.025, y = -0.1, just = "right", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
grid.text(paste(axis.x.labels[2],"bp"), x = 1.015, y = -0.1, just = "left", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
if(config.var$disp.color.ref) {
#Color red the reference
grid.xaxis(at = gbl.var$mydata.ref.pos, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width, col="darkorchid1"))
}
#Remove trailing tick mark
grid.edit("axis.x.labels", gp = gpar(col = "white"))
}
else {
if(! is.null(config.var$mydata.large.file)){
grid.xaxis(at = gbl.var$sorted.mydata.large.pos.zoom, label = FALSE, gp = gpar(col="grey", cex = gbl.var$cex.factor, lwd = gbl.var$line.width))
}
grid.xaxis(at = axis.x.labels, label = FALSE, gp = gpar(cex = gbl.var$cex.factor), name = "axis.x.labels")
grid.xaxis(at = gbl.var$sorted.mydata.pos.zoom, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width))
grid.text(paste(axis.x.labels[1],"bp"), x = -0.025, y = -0.09, just = "right", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
grid.text(paste(axis.x.labels[2],"bp"), x = 1.015, y = -0.09, just = "left", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
if(config.var$disp.color.ref) {
#Color red the reference
grid.xaxis(at = gbl.var$mydata.ref.pos, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width, col="darkorchid1"))
}
#Remove trailing tick mark
grid.edit("axis.x.labels", gp = gpar(col = "white"))
}
#------------------ X-AXIS -----------------------
#-------------------EQUIDISPOS COORDINATE BEGINS-------------
gbl.var$equidis.pos <- NULL
#DEBUG STATEMENT
# if (config.var$verbose) cat("length(gbl.var$equidis.pos) ", length(gbl.var$equidis.pos), "\n")
# if (config.var$verbose) cat("length(gbl.var$mydata.num) ", length(gbl.var$mydata.pos), "\n")
gbl.var$mydata.num <- length(gbl.var$sorted.mydata.pos)
if(config.var$disp.cormatrixmap) {
pos.increment <- (gbl.var$max.x - gbl.var$min.x) / gbl.var$mydata.num
#Attempt to center the MYDATA labels
start.pos <- gbl.var$min.x
for(i in 0:(gbl.var$mydata.num - 1)) {
gbl.var$equidis.pos <- c(gbl.var$equidis.pos, pos.increment * i + start.pos)
}
} else {
pos.increment <- (gbl.var$max.x - gbl.var$min.x) / gbl.var$mydata.num
#Attempt to center the MYDATA labels
start.pos <- gbl.var$min.x
for(i in 0:(gbl.var$mydata.num - 1)) {
gbl.var$equidis.pos <- c(gbl.var$equidis.pos, pos.increment * i + start.pos)
}
}
#----------------- Y-AXIS --------------------
if(config.var$lab.Y == "ln") {
if(config.var$disp.marker.lines) {
initial.abline <- 0.1
while(-log(initial.abline) < gbl.var$axis.y[1]) {
initial.abline <- initial.abline / 10
#DEBUG STATEMENT
if (config.var$verbose) cat("initial.abline 1", initial.abline, "\n")
}
while(-log(initial.abline) < max(gbl.var$axis.y)) {
#DEBUG STATEMENT
if (config.var$verbose) cat("initial.abline 2", initial.abline, "\n")
grid.lines(x = gbl.var$axis.x, y = -log(initial.abline), default.units = "native", gp = gpar(lty = "dashed", lwd = gbl.var$line.width, col="gainsboro"))
initial.abline <- initial.abline / 10
}
}
} else {
if(config.var$disp.marker.lines) {
initial.abline <- 0.1
while(-log10(initial.abline) < gbl.var$axis.y[1]) {
initial.abline <- initial.abline / 10
}
while(-log10(initial.abline) < max(gbl.var$axis.y)) {
grid.lines(x = gbl.var$axis.x, y = -log10(initial.abline), default.units = "native", gp = gpar(lty = "dashed", lwd = gbl.var$line.width, col="gainsboro"))
initial.abline <- initial.abline / 10
}
}
}
#----------- X-AXIS of THRESHOLD of pvalue
if(config.var$pval.threshold != 0 & config.var$pval.threshold > config.var$disp.pval.threshold){
grid.lines(x = gbl.var$axis.x, y = config.var$pval.threshold, default.units = "native", gp = gpar(lty = "dashed", lwd = gbl.var$line.width , col="red"))
}
#----------- X-AXIS of the second THRESHOLD of pvalue
if(config.var$pval.threshold.2 != 0 & config.var$pval.threshold.2 > config.var$disp.pval.threshold){
grid.lines(x = gbl.var$axis.x, y = config.var$pval.threshold.2, default.units = "native", gp = gpar(lty = "dashed", lwd = gbl.var$line.width , col="orange"))
}
#----------- X-AXIS of base
grid.lines(x = gbl.var$axis.x, y = gbl.var$axis.y[1], default.units = "native", gp = gpar(lwd = gbl.var$line.width))
grid.yaxis(at = gbl.var$axis.y, label = gbl.var$axis.y, gp = gpar(fontsize = gbl.var$font.size, lwd = gbl.var$line.width))
#----------- WRITE LABEL for Y-AXIS
if(config.var$lab.Y == "ln") {
grid.text("-ln(P-value)",
x = -0.1,
y = 0.5,
rot = 90,
gp = gpar(fontsize = (gbl.var$font.size * config.var$font.factor),
fontface = "bold"))
} else {
grid.text("-log10(P-value)",
x = -0.1,
y = 0.5,
rot = 90,
gp = gpar(fontsize = (gbl.var$font.size * config.var$font.factor),
fontface = "bold"))
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.AXIS.DATA\n")
}
#------------------- DRAW ANNOTATION -----------------------
draw.plot.annotation <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.ANNOTATION\n")
popViewport()
top.vp <- gbl.var$top.vp
annotation.vp.cormatrixmap <- viewport(height = 0.95,
width = 1,
layout.pos.row = 4,
layout.pos.col = 2,
name = "annotation.vp.cormatrixmap")
annotation.vp.nocormatrixmap <- viewport(height = 0.95,
width = 1,
layout.pos.row = 5,
layout.pos.col = 2,
name = "annotation.vp.nocormatrixmap")
annotation.vp.cormatrixmap.nopval <- viewport(height = 0.95,
width = 1,
layout.pos.row = 3,
layout.pos.col = 2,
name = "annotation.vp.cormatrixmap.nopval")
if(config.var$disp.cormatrixmap) {
if(config.var$disp.pvalueplot) {
pushViewport(vpTree(top.vp, vpList(annotation.vp.cormatrixmap)))
pushViewport(annotation.vp.cormatrixmap)
} else {
pushViewport(vpTree(top.vp, vpList(annotation.vp.cormatrixmap.nopval)))
pushViewport(annotation.vp.cormatrixmap.nopval)
}
}
else {
pushViewport(vpTree(top.vp, vpList(annotation.vp.nocormatrixmap)))
pushViewport(annotation.vp.nocormatrixmap)
}
size_gviz <- 0
if( ! is.null(gbl.var$listtracks_gviz)){
size_gviz <- length(gbl.var$listtracks_gviz) * 2
}
size_gviz_user <- 0
if(!is.null(config.var$biofeat.user.file)){
# gbl.var <- create.tracks.user(config.var,gbl.var)
size_gviz_user <- length(gbl.var$listtracks_user)
}
size_trackviewer <- 0
if( ! is.null(gbl.var$listtracks_trackviewer)){
size_trackviewer <- length(gbl.var$listtracks_trackviewer)
}
size_ggbio <- 0
if( ! is.null(gbl.var$listtracks_ggbio)){
size_ggbio <- length(gbl.var$listtracks_ggbio) * 4
}
total_tracks <- size_gviz + size_trackviewer + size_ggbio
if (config.var$verbose) cat("Number of track", total_tracks, "GVIZ", size_gviz,"\n")
annotvp <-viewport(layout=grid.layout(4, 1, heights=unit(c(size_gviz,size_ggbio,size_trackviewer,size_gviz_user),"null")),name = "annotviewport")
gvizviewport <- viewport(layout.pos.col = 1, layout.pos.row = 1, name = "gvizviewport")
ggbioviewport <- viewport(layout.pos.col = 1, layout.pos.row = 2, name = "ggbioviewport")
trackviewerviewport <- viewport(layout.pos.col = 1, layout.pos.row = 3, name = "trackviewerviewport")
gvizuserviewport <- viewport(layout.pos.col = 1, layout.pos.row = 4, name = "gvizuserviewport")
if(config.var$disp.cormatrixmap) {
if(config.var$disp.pvalueplot) {
pushViewport(vpTree(annotation.vp.cormatrixmap, vpList(gvizviewport, ggbioviewport, trackviewerviewport,gvizuserviewport)))
} else {
pushViewport(vpTree(annotation.vp.cormatrixmap.nopval, vpList(gvizviewport, ggbioviewport, trackviewerviewport,gvizuserviewport)))
}
}
else {
pushViewport(vpTree(annotation.vp.nocormatrixmap, vpList(gvizviewport, ggbioviewport, trackviewerviewport,gvizuserviewport)))
}
pushViewport(annotvp)
if(! (is.null(gbl.var$listtracks_gviz))){
seekViewport("annotviewport")
pushViewport(gvizviewport)
plotTracks(gbl.var$listtracks_gviz, from=gbl.var$min.x, to=gbl.var$max.x,panel.only=TRUE,add=TRUE, fontsize=config.var$fontsize.gviz)
}
if(! (is.null(gbl.var$listtracks_ggbio))){
seekViewport("annotviewport")
pushViewport(ggbioviewport)
l.g <- lapply(gbl.var$listtracks_ggbio, function(x){
ggplotGrob(x)
})
# grid.rect(gp=gpar(col="blue"))
grid.arrange(do.call(arrangeGrob, c(l.g, list(nrow = size_ggbio/4, ncol = 1))),newpage=FALSE)
#tracks(gbl.var$listtracks_ggbio)
}
if(! (is.null(gbl.var$listtracks_trackviewer))){
seekViewport("annotviewport")
pushViewport(trackviewerviewport)
viewTracks(trackList(gbl.var$listtracks_trackviewer),chromosome=gbl.var$mydata.chr,start=gbl.var$min.x, end=gbl.var$max.x,newpage=FALSE)
}
if(! (is.null(gbl.var$listtracks_user))){
seekViewport("annotviewport")
pushViewport(gvizuserviewport)
plotTracks(gbl.var$listtracks_user, from=gbl.var$min.x, to=gbl.var$max.x,panel.only=TRUE,add=TRUE, fontsize=config.var$fontsize.gviz)
}
popViewport()
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.ANNOTATION\n")
}
#------------------- DRAW DATA via GGBIO -----------------------
draw.plot.mydata.ggbio <- function(config.var, gbl.var,numfile) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.MYDATA\n")
split.mydata.file <- gbl.var$split.mydata.file
gbl.var <-read.file.mydata(split.mydata.file[[1]],config.var, gbl.var,numfile)
# if (config.var$verbose) cat("READ ",i," MYDATA file \n")
mydata.data <- gbl.var$mydata.data
mydata.pv <- log(mydata.data[,4])
startlist<-mydata.data[,3]
endlist<-mydata.data[,3]
id<-mydata.data[,1]
cprange<-GRanges(gbl.var$mydata.chr,IRanges(startlist,endlist))
# startlarge<-start-50000
# endlarge<-end+50000
cpidrange<-GRanges(gbl.var$mydata.chr,IRanges(startlist,endlist),"*",id)
data<-DataTrack(range=cprange,start,end,data=mydata.pv,name="CpG pvalue",cex=.16)
namedata_track <- AnnotationTrack(chromosome=gbl.var$mydata.chr,strand ="*",start=startlist,end=startlist,
feature="CpG",group=id,id=id, name = "feature")
return(list(data,namedata_track))
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.MYDATA\n")
}
#-------------------DRAW SINGLE MYDATA------------------
draw.plot.grid.mydata <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.GRID.MYDATA\n")
# Grab from configuration is available
if(is.null(config.var$symbol.factor)) {
tmp.cex.factor.symbol = gbl.var$cex.factor.symbol
} else {
tmp.cex.factor.symbol = config.var$symbol.factor
}
list.colors.bar <- create.color.bar(config.var, gbl.var)
color.cut <- list.colors.bar$color.cut
color.cut.ref <- list.colors.bar$color.cut.ref
#z<-color.cut[,mydata.num]
# gbl.var$fill.list[gbl.var$cur.sample]
format <- as.character(gbl.var$split.format[[1]][gbl.var$cur.sample])
if(config.var$disp.mydata) {
if(config.var$disp.type == "symbol") {
if(gbl.var$cur.sample == 1) {
#------------- DATA of INTERET
for (i in 1:nrow(gbl.var$mydata.data)) {
name.test <-gbl.var$mydata.data$MYDATA.NAME[i]
position <- gbl.var$mydata.hash.names.pos[[name.test]]
#cat ("color",i, " ", color.cut.ref[i],"\n")
if ((gbl.var$mydata.data$MYDATA.PVAL[i] > config.var$disp.pval.threshold) &
(gbl.var$mydata.data$MYDATA.PVAL[i] != 0) &
(position > (gbl.var$min.x - 1)) &
(position < (gbl.var$max.x + 1)) ) {
#---- ASSOCIATION COLOR and SIZE
mycolor <- color.cut.ref[i]
myasso <- 0
if(! is.null(config.var$disp.association)){
if(as.logical(gbl.var$split.association[[1]][gbl.var$cur.sample]) & (grepl("asso", format)[1])) {
if (config.var$verbose) cat("Association ", gbl.var$mydata.data$MYDATA.ASSO[i]," \n")
mycolor <- gbl.var$fill.list[gbl.var$cur.sample]
myasso <- gbl.var$mydata.data$MYDATA.ASSO[i]
if(grepl("-", myasso)[1]) {
if(config.var$verbose) cat("Opposited color \n")
mycolor.tmp <- opposite(mycolor,plot=FALSE)[2]
mycolor <- mycolor.tmp
} else if (gbl.var$mydata.data$MYDATA.ASSO[i] == "0") {
mycolor.tmp <- "black"
mycolor <- mycolor.tmp
}
}
}
mycex <- tmp.cex.factor.symbol
if(! is.null(config.var$disp.beta.association)){
myassoorig <- gbl.var$mydata.data$MYDATA.ASSO.ORIGINAL[i]
if(is.integer(myassoorig)){
myasso.zscore <- (myassoorig - gbl.var$mean.beta)/gbl.var$sd.beta
myasso.zscore.abs <- abs(myasso.zscore)
mycex <- tmp.cex.factor.symbol + gbl.var$myfactor.beta*myasso.zscore.abs
}
}
# if (config.var$verbose) cat("config.var$mydata.ref",config.var$mydata.ref,"\n")
# if (config.var$verbose) cat("gbl.var$mydata.data$MYDATA.NAME[i]",gbl.var$mydata.data$MYDATA.NAME[i],"\n")
# if (config.var$verbose) cat("My data",i,"vs my ref", gbl.var$mydata.best.position,"\n")
ref.print <- "FALSE"
if (exists("config.var$mydata.ref") & !is.null(config.var$mydata.ref) ) {
if (length(config.var$mydata.ref) > 0 & (gbl.var$mydata.data$MYDATA.NAME[i] == config.var$mydata.ref)){
ref.print <- "TRUE"
}
} else if ( (length(config.var$mydata.ref) > 0 ) & (i == gbl.var$mydata.best.position)){
ref.print <- "TRUE"
}
if (i == gbl.var$mydata.best.position){
ref.print <- "TRUE"
}
if (as.logical(ref.print)) {
grid.points(position,
gbl.var$mydata.data$MYDATA.PVAL[i],
pch = gbl.var$symbol.list[gbl.var$cur.sample],
gp = gpar(col = mycolor,
cex = tmp.cex.factor.symbol,
fill = "black" ,
lwd = gbl.var$line.width))
if(!is.null(config.var$disp.region)){
if(as.logical(gbl.var$split.region[[1]][gbl.var$cur.sample]) & (grepl("region", format)[1])){
# if (config.var$verbose) cat("format",format,"\n")
position.start <- gbl.var$mydata.hash.names.start[[name.test ]]
position.end <- gbl.var$mydata.hash.names.end[[name.test ]]
if(position.start < (gbl.var$min.x - 1)){
position.start <- (gbl.var$min.x - 1)
}
if(position.end > (gbl.var$max.x + 1)){
position.end <- (gbl.var$max.x + 1)
}
grid.lines(x = c(position.start,position.end),
y = c(gbl.var$mydata.data$MYDATA.PVAL[i],gbl.var$mydata.data$MYDATA.PVAL[i]),
default.units = "native", gp = gpar(lty = "solid", lwd = gbl.var$line.width, col=mycolor))
}
}
}else {
grid.points(position,
gbl.var$mydata.data$MYDATA.PVAL[i],
pch = gbl.var$symbol.list[gbl.var$cur.sample],
gp = gpar(col = "black",
cex = tmp.cex.factor.symbol,
fill = mycolor ,
lwd = gbl.var$line.width))
if(!is.null(config.var$disp.region)){
if(as.logical(gbl.var$split.region[[1]][gbl.var$cur.sample]) & (grepl("region", format)[1] )){
position.start <- gbl.var$mydata.hash.names.start[[name.test ]]
position.end <- gbl.var$mydata.hash.names.end[[name.test ]]
if(position.start < (gbl.var$min.x - 1)){
position.start <- (gbl.var$min.x - 1)
}
if(position.end > (gbl.var$max.x + 1)){
position.end <- (gbl.var$max.x + 1)
}
grid.lines(x = c(position.start,position.end),
y = c(gbl.var$mydata.data$MYDATA.PVAL[i],gbl.var$mydata.data$MYDATA.PVAL[i]),
default.units = "native", gp = gpar(lty = "solid", lwd = gbl.var$line.width, col=mycolor))
}
}
}
}
}
} else {
for (i in 1:nrow(gbl.var$mydata.data)) {
name.test <-gbl.var$mydata.data$MYDATA.NAME[i]
position <- gbl.var$mydata.hash.names.pos[[name.test ]]
if ((gbl.var$mydata.data$MYDATA.PVAL[i] > config.var$disp.pval.threshold) &
(gbl.var$mydata.data$MYDATA.PVAL[i] != 0) &
(position > (gbl.var$min.x - 1)) &
(position < (gbl.var$max.x + 1)) ) {
#---- ASSOCIATION COLOR and size
mycolor <- color.cut.ref[i]
myasso <- 0
if(! is.null(config.var$disp.association)){
if( as.logical(gbl.var$split.association[[1]][gbl.var$cur.sample]) & (grepl("asso", format)[1])) {
mycolor <- gbl.var$fill.list[gbl.var$cur.sample]
myasso <- gbl.var$mydata.data$MYDATA.ASSO[i]
if (grepl("-", myasso)[1]) {
mycolor.tmp <- opposite(mycolor,plot=FALSE)[2]
mycolor <- mycolor.tmp
} else if (gbl.var$mydata.data$MYDATA.ASSO[i] == "0") {
mycolor.tmp <- "black"
mycolor <- mycolor.tmp
}
}
}
mycex <- tmp.cex.factor.symbol
if(! is.null(config.var$disp.beta.association)){
myassoorig <- gbl.var$mydata.data$MYDATA.ASSO.ORIGINAL[i]
if(is.integer(myassoorig)){
myasso.zscore <- (myassoorig - gbl.var$mean.beta)/gbl.var$sd.beta
myasso.zscore.abs <- abs(myasso.zscore)
mycex <- tmp.cex.factor.symbol + gbl.var$myfactor.beta*myasso.zscore.abs
}
}
if (is.na(gbl.var$symbol.list[gbl.var$cur.sample])) {
grid.points(position,
gbl.var$mydata.data$MYDATA.PVAL[i],
pch = 25,
gp = gpar(col = gbl.var$color.list[gbl.var$cur.sample],
cex = tmp.cex.factor.symbol,
fill = mycolor,
lwd = gbl.var$line.width))
}
else {
grid.points(position,
gbl.var$mydata.data$MYDATA.PVAL[i],
pch = gbl.var$symbol.list[gbl.var$cur.sample],
gp = gpar(col = gbl.var$color.list[gbl.var$cur.sample],
cex = tmp.cex.factor.symbol,
fill = mycolor,
lwd = gbl.var$line.width))
}
if(! is.null(config.var$disp.region)){
if(as.logical(gbl.var$split.region[[1]][gbl.var$cur.sample]) & (grepl("region", format)[1] )){
position.start <- gbl.var$mydata.hash.names.start[[name.test ]]
position.end <- gbl.var$mydata.hash.names.end[[name.test ]]
if(position.start < (gbl.var$min.x - 1)){
position.start <- (gbl.var$min.x - 1)
}
if(position.end > (gbl.var$max.x + 1)){
position.end <- (gbl.var$max.x + 1)
}
grid.lines(x = c(position.start,position.end),
y = c(gbl.var$mydata.data$MYDATA.PVAL[i],gbl.var$mydata.data$MYDATA.PVAL[i]),
default.units = "native", gp = gpar(lty = "solid", lwd = gbl.var$line.width, col=mycolor))
}
}
}
}
}
}
else {
dev.off()
stop("Invalid display type: ", config.var$disp.type, "\n")
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.GRID.MYDATA\n")
}
#-------------------DRAW LARGE MYDATA------------------
draw.plot.grid.mydata.large <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.GRID.MYDATA.large\n")
# Grab from configuration is available
if(is.null(config.var$symbol.factor)) {
tmp.cex.factor.symbol = gbl.var$cex.factor.symbol
} else {
tmp.cex.factor.symbol = config.var$symbol.factor
}
format <- as.character(gbl.var$large.split.format[[1]][gbl.var$cur.sample.large])
if(config.var$disp.mydata) {
if(config.var$disp.type == "symbol") {
#------------- DATA LARGE
if(! is.null(config.var$mydata.large.file)) {
for (i in 1:nrow(gbl.var$mydata.large.data)) {
#---- ASSOCIATION COLOR
mycolor <- gbl.var$large.fill.list[gbl.var$cur.sample.large]
myassolarge <- 0
if(!is.null(config.var$disp.association.large)){
if(as.logical(gbl.var$large.split.association[[1]][gbl.var$cur.sample.large]) & (grepl("asso", format)[1])) {
if (config.var$verbose) cat("Association ",gbl.var$mydata.large.data$MYDATA.ASSO[i]," \n")
myassolarge <- gbl.var$mydata.large.data$MYDATA.ASSO[i]
if (grepl("-", myassolarge)[1]) {
mycolor.fill.tmp <- opposite(mycolor,plot=FALSE)[2]
mycolor <- mycolor.fill.tmp
} else if (gbl.var$mydata.large.data$MYDATA.ASSO[i] == "0") {
mycolor.fill.tmp <- "black"
mycolor <- mycolor.fill.tmp
}
}
}
mycex <- tmp.cex.factor.symbol
if(! is.null(config.var$disp.beta.association.large)){
myassolargeorig <- gbl.var$mydata.large.data$MYDATA.ASSO.ORIGINAL[i]
if(is.integer(myassolargeorig)){
myassolarge.zscore <- (myassolargeorig - gbl.var$mean.beta)/gbl.var$sd.beta
myassolarge.zscore.abs <- abs(myassolarge.zscore)
cat("original cex",tmp.cex.factor.symbol,"factor",gbl.var$myfactor.beta, " absolue ",myassolarge.zscore.abs,"\n")
mycex <- tmp.cex.factor.symbol + gbl.var$myfactor.beta*myassolarge.zscore.abs
cat("cex",mycex,"ref",tmp.cex.factor.symbol,"\n")
}
}
name.test <-gbl.var$mydata.large.data$MYDATA.NAME[i]
position <- gbl.var$mydata.large.hash.names.pos[[name.test]]
# if (config.var$verbose) cat("position",position)
if ((gbl.var$mydata.large.data$MYDATA.PVAL[i] > config.var$disp.pval.threshold) &
(gbl.var$mydata.large.data$MYDATA.PVAL[i] != 0) &
(position > (gbl.var$min.x - 1)) &
(position < (gbl.var$max.x + 1)) &
(gbl.var$mydata.large.data$MYDATA.PVAL[i] > (gbl.var$min.y - 1)) &
(gbl.var$mydata.large.data$MYDATA.PVAL[i] < (gbl.var$max.y + 1)) ) {
# if (config.var$verbose) cat("config.var$mydata.ref",config.var$mydata.ref,"\n")
# if (config.var$verbose) cat("gbl.var$mydata.data$MYDATA.NAME[i]",gbl.var$mydata.data$MYDATA.NAME[i],"\n")
if (is.na(gbl.var$large.symbol.list[gbl.var$cur.sample.large])) {
grid.points(position,
gbl.var$mydata.large.data$MYDATA.PVAL[i],
pch = 21,
gp = gpar(col = gbl.var$large.color.list[gbl.var$cur.sample.large],
cex = tmp.cex.factor.symbol,
fill = mycolor,
lwd = gbl.var$line.width))
} else {
grid.points(position,
gbl.var$mydata.large.data$MYDATA.PVAL[i],
pch = gbl.var$large.symbol.list[gbl.var$cur.sample.large],
gp = gpar(col = gbl.var$large.color.list[gbl.var$cur.sample.large],
cex = tmp.cex.factor.symbol,
fill = mycolor,
lwd = gbl.var$line.width))
}
# if (config.var$verbose) cat("format ",format,"\n")
# if (config.var$verbose) cat("Sample",gbl.var$cur.sample.large,"\n")
# if(grepl("region", format)[1] ){
# if (config.var$verbose) cat("format ",format,"\n")
# }
if (grepl("region", format)[1]){
if(! is.null(config.var$disp.region.large)) {
region.print <- "FALSE"
if(! is.null(config.var$disp.region.large)){
# if(exists("gbl.var$large.split.region[[1]][gbl.var$cur.sample.large])"){
#if(!is.null(gbl.var$large.split.region[[1]][gbl.var$cur.sample.large])){
if(as.logical(gbl.var$large.split.region[[1]][gbl.var$cur.sample.large])){
region.print <- "TRUE"
}
if(as.logical(region.print) ){
if (config.var$verbose) cat("region",gbl.var$large.split.region[[1]][gbl.var$cur.sample.large],"\n")
position.start <- gbl.var$mydata.large.hash.names.start[[name.test]]
position.end <- gbl.var$mydata.large.hash.names.end[[name.test]]
if(position.start < (gbl.var$min.x - 1)){
position.start <- (gbl.var$min.x - 1)
}
if(position.end > (gbl.var$max.x + 1)){
position.end <- (gbl.var$max.x + 1)
}
if (config.var$verbose) cat("position.start ",position.start,"\n")
if (config.var$verbose) cat("position.end ",position.end,"\n")
if (config.var$verbose) cat("y",gbl.var$mydata.large.data$MYDATA.PVAL[i],"\n")
if (config.var$verbose) cat("axis.x ", gbl.var$axis.x,"\n")
grid.lines(x = c(position.start,position.end),
y = c(gbl.var$mydata.large.data$MYDATA.PVAL[i],gbl.var$mydata.large.data$MYDATA.PVAL[i]),
default.units = "native", gp = gpar(lty = "solid", lwd = gbl.var$line.width, col=mycolor))
}
}
}
}
}
}
}
}
else {
dev.off()
stop("Invalid display type: ", config.var$disp.type, "\n")
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.GRID.MYDATA.large\n")
}
#-------------------DRAW CORMATRIX plot------------------
draw.plot.cormatrix.plot <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.CORMATRIX.PLOT\n")
cormatrix.matrix <- gbl.var$cormatrix.data
matrix.rows <- dim(cormatrix.matrix)[1]
matrix.cols <- dim(cormatrix.matrix)[2]
list.colors.bar <- create.color.bar(config.var, gbl.var)
color.cut <- list.colors.bar$color.cut
cormatrix.key <- list.colors.bar$cormatrix.key
map.label.ldtype <- list.colors.bar$map.label.ldtype
map.label.distance <- list.colors.bar$map.label.distance
#cat ("color",1, " ", color.cut)
x.x <- (1:matrix.cols)/matrix.cols
y.y <- (1:matrix.rows)/matrix.rows
right <- rep(x.x, nrow(gbl.var$general.data))
top <- rep(y.y, each=matrix.cols)
image.rect <- rectGrob(x=right,
y=top,
width=1/matrix.cols,
height=1/matrix.rows,
just=c("right", "top"),
gp=gpar(col=NULL,
fill=color.cut,
lty="blank"),
name="image.rect")
#seq.x <- c(1*(1/gbl.var$mydata.num), 1)
#seq.y <- c(0, (1 - (1/gbl.var$mydata.num)))
tmp.mydata.num <- gbl.var$mydata.num
seq.x.names <- seq((1/tmp.mydata.num), 1, by=(1/tmp.mydata.num))
seq.y.names <- seq(0, (1 - (1/tmp.mydata.num)), by=(1/tmp.mydata.num))
#The condition for the tmp.mydata.num is met in the original construction of the sequence
if(tmp.mydata.num > 50) {
tmp.x.factor <- seq.x.names[1]
seq.x.names <- seq.x.names + tmp.x.factor/2
seq.y.names <- seq.y.names - tmp.x.factor/2
} else if(tmp.mydata.num < 50) {
tmp.x.factor <- (seq.x.names[1] - 0.02)/2 + 0.02
tmp.y.factor <- (seq.x.names[1] - 0.02)/2
seq.x.names <- seq(tmp.x.factor, (1 - tmp.y.factor), by=(1/tmp.mydata.num))
seq.y.names <- seq(tmp.y.factor, (1 - tmp.y.factor), by=(1/tmp.mydata.num))
}
mydata.names.pos.x <- (1:gbl.var$mydata.num)/gbl.var$mydata.num
mydata.names.pos.y <- ((1:gbl.var$mydata.num)/gbl.var$mydata.num - 1/gbl.var$mydata.num)
###Factor for the size of name
# if(is.null(config.var$font.factor)) {
# tmp.font.factor = (gbl.var$cex.factor - 0.5)
# } else {
# tmp.font.factor = as.numeric(config.var$font.factor)
#}
tmp.font.factor = (gbl.var$cex.factor - 0.5)
if (config.var$disp.mydata.names) {
if( length(gbl.var$sorted.mydata.names) < 30) {
list.name <- paste(" ",gbl.var$sorted.mydata.names)
name.ref <- paste(" ",gbl.var$sorted.mydata.names[gbl.var$mydata.ref.pos])
} else {
list.name <- paste("",gbl.var$sorted.mydata.names)
name.ref <- paste("",gbl.var$sorted.mydata.names[gbl.var$mydata.ref.pos])
}
rot.name <- -45
#if (config.var$cormatrix.format == "raw") {
# rot.name <- 135
#}
mydata.names.cormatrix.sec <- textGrob(rev(list.name),
x = seq.x.names[1:gbl.var$mydata.num],
y = seq.y.names[1:gbl.var$mydata.num],
rot=rot.name,
gp=gpar(cex = tmp.font.factor),
just = c("left"),
name="mydata.names.cormatrix.sec")
if(config.var$disp.color.ref) {
#REFERENCE
mydata.names.cormatrix.sec.ref <- textGrob(rev(name.ref),
x = seq.x.names[gbl.var$mydata.ref.pos],
y = seq.y.names[gbl.var$mydata.ref.pos],
rot=rot.name,
gp=gpar(cex = tmp.font.factor,col="darkorchid1"),
just = c("left"),
name="mydata.names.cormatrix.sec")
}
}
popViewport()
#67.5
##### VIEW PORT FOR LD MAP
cormatrix.map.vp <- viewport(y = unit(0.415, "npc"),
x = unit(0.471875, "npc"),
width = unit(0.7, "snpc"),
height = unit(0.7, "snpc"),
angle = 67.5,
just = c("center", "center"),
name = "cormatrix.map.vp")
if (config.var$disp.mydata.names) {
if(config.var$disp.color.ref) {
cormatrix.map <- gTree(children=gList(image.rect, mydata.names.cormatrix.sec, mydata.names.cormatrix.sec.ref), just=c("center", "bottom"), vp=cormatrix.map.vp, name="cormatrix.map")
} else {
cormatrix.map <- gTree(children=gList(image.rect, mydata.names.cormatrix.sec), just=c("center", "bottom"), vp=cormatrix.map.vp, name="cormatrix.map")
}
} else {
cormatrix.map <- gTree(children=gList(image.rect), just=c("center"), vp=cormatrix.map.vp, name="cormatrix.map")
}
gene.map.vp <- viewport(name = "gene.map.vp")
gene.map <- gTree(children=gList(map.label.ldtype, map.label.distance), vp = gene.map.vp, name="gene.map")
pushViewport(cormatrix.map.vp)
grid.draw(cormatrix.map)
popViewport()
pushViewport(gene.map.vp)
grid.draw(gene.map)
if(config.var$disp.color.bar) {
#DEBUG STATEMENT
# if (config.var$verbose) cat("is.null(cormatrix.key) ", is.null(cormatrix.key), "\n")
grid.draw(cormatrix.key)
}
popViewport()
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.CORMATRIX.PLOT\n")
}
#-------------------DRAW LEGEND----------------------------
draw.legend <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.LEGEND\n")
#DEBUG STATEMENT
# if (config.var$verbose) cat("gbl.var$font.size ", gbl.var$font.size, "\n")
if(config.var$disp.cormatrixmap) {
legend.vp <- viewport(x = 0.5, y = -2, height = 1, width = 1, name = "legend.vp")
}
else {
legend.vp<- viewport(x = 0.5, y = 0.05, height = 1, width = 1, name = "legend.vp")
}
pushViewport(legend.vp)
#-------------------LEGEND SAMPLES BEGINS-----------------------
legend.samples.list <- NULL
legend.samples <- gTree(children=NULL,
just=c("center", "bottom"), vp=legend.vp,
name="legend.samples")
samples <- gbl.var$samples
if(samples <= 8) {
y.pos.sec.row.correction <- 0
x.pos.sec.row.correction <- 0
#--------------- LEGEND FOR REFERENCE
# if (config.var$verbose) cat("Reference \n")
#Ensure that labels do not overlap by moving them
if(config.var$disp.cormatrixmap) {
y.pos <- .8
x.pos <- 0.75
} else {
y.pos <- -0.3125 + y.pos.sec.row.correction
x.pos <- -0.19 + x.pos.sec.row.correction
}
label.text.ref <- gbl.var$mydata.data$MYDATA.NAME[which(gbl.var$mydata.data$LOC == gbl.var$mydata.ref.pos)]
label.sample.text <- textGrob(label.text.ref,
x = (x.pos + 0.035),
y = y.pos,
just=("left"),
gp = gpar(fontsize = gbl.var$font.size *0.75 * config.var$font.factor))
#FOR LD adjust is .3
#FOR NO-LD adjust is
label.sample.symbol <- pointsGrob(x = x.pos,
y = y.pos,
pch = 21,
gp = gpar(col = "darkorchid1",
cex = (gbl.var$cex.factor - 0.5),
lwd = gbl.var$line.width,
fill = "black"))
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.text
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.symbol
#All samples
# if (config.var$verbose) cat("All samples \n")
for(i in 1:samples) {
if(i > 3) {
x.pos.sec.row.correction <- -1.5
y.pos.sec.row.correction <- -.04
}
#label.text <- substr(gbl.var$split.sample.labels[[1]][i],1, 30)
label.text <- gbl.var$split.sample.labels[[1]][i]
#Ensure that labels do not overlap by moving them
if(config.var$disp.cormatrixmap) {
y.pos <- .8 + 0.1 * i
x.pos <- 0.75
} else {
y.pos <- -0.3125 + y.pos.sec.row.correction
x.pos <- -0.19 + 0.35* i + x.pos.sec.row.correction
}
label.sample.text <- textGrob(label.text,
x = (x.pos + 0.035),
y = y.pos,
just=("left"),
gp = gpar(fontsize = (gbl.var$font.size)*0.75 * (config.var$font.factor)))
if(is.na(gbl.var$symbol.list[i])) {
gbl.var$symbol.list[i] <- "circle-fill"
}
#FOR LD adjust is .3
#FOR NO-LD adjust is
label.sample.symbol <- pointsGrob(x = x.pos,
y = y.pos,
pch = gbl.var$symbol.list[i],
gp = gpar(col = "black",
cex = (gbl.var$cex.factor - 0.5),
lwd = gbl.var$line.width,
fill = gbl.var$fill.list[i]))
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.text
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.symbol
}
#--------------- LEGEND LARGE DATA
if(! is.null(config.var$mydata.large.file)){
large.samples <- gbl.var$large.samples
for(i in 1:large.samples) {
if((samples + i) > 3) {
x.pos.sec.row.correction <- -1.5
y.pos.sec.row.correction <- -.04
}
#label.text <- substr(gbl.var$large.split.sample.labels[[1]][i], 1, 30)
label.text <- gbl.var$large.split.sample.labels[[1]][i]
#Ensure that labels do not overlap by moving them
if(config.var$disp.cormatrixmap) {
y.pos <- .8 + 0.1 * (samples + i )
x.pos <- 0.75
} else {
y.pos <- -0.3125 + y.pos.sec.row.correction
x.pos <- -0.19 + 0.35* ( samples + i ) + x.pos.sec.row.correction
}
label.sample.text <- textGrob(label.text,
x = (x.pos + 0.035),
y = y.pos,
just=("left"),
gp = gpar(fontsize = (gbl.var$font.size) *0.75 * config.var$font.factor))
if(is.na(gbl.var$large.symbol.list[i])) {
gbl.var$large.symbol.list[i] <- 24
}
#FOR LD adjust is .3
#FOR NO-LD adjust is
label.sample.symbol <- pointsGrob(x = x.pos,
y = y.pos,
pch = gbl.var$large.symbol.list[i],
gp = gpar(col = gbl.var$large.color.list[i],
cex = (gbl.var$cex.factor - 0.5),
lwd = gbl.var$line.width,
fill = gbl.var$large.fill.list[i]))
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.text
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.symbol
}
}
class(legend.samples.list) <- c("gList")
legend.glist.samples <- legend.samples.list
legend.samples <- gTree(children=legend.glist.samples,
just=c("left", "bottom"),
vp=legend.vp,
name="legend.samples")
grid.draw(legend.samples)
}
popViewport()
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.LEGEND\n")
}
#-------------------DRAW MYDATA NAME----------------------------
#draw MYDATA labels
draw.plot.grid.mydata.names <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.GRID.MYDATA.NAMES\n")
tmp.correction.factor <- gbl.var$equidis.pos[1] * 10^(gbl.var$cur.exp - 9) * (1 + config.var$connecting.lines.adj)
#DEBUG STATEMENT
# if (config.var$verbose) cat("config.var$disp.cormatrixmap ", config.var$disp.cormatrixmap, "\n")
if (config.var$verbose) cat("length(gbl.var$sorted.mydata.names) ", length(gbl.var$sorted.mydata.names), "\n")
# if (config.var$verbose) cat("tmp.correction.factor ", tmp.correction.factor, "\n")
# if (config.var$verbose) cat("gbl.var$axis.y[1] ", gbl.var$axis.y[1], "\n")
if(!config.var$disp.cormatrixmap) {
if( length(gbl.var$sorted.mydata.names) < 30) {
list.name <- paste(" ",gbl.var$sorted.mydata.names)
name.ref <- paste(" ",gbl.var$sorted.mydata.names[gbl.var$mydata.ref.pos])
} else {
list.name <- paste("",gbl.var$sorted.mydata.names)
name.ref <- paste("",gbl.var$sorted.mydata.names[gbl.var$mydata.ref.pos])
}
rot.name <- 90
if (config.var$cormatrix.format == "raw") {
rot.name <- -90
}
if(config.var$image.size == 3.5) {
if( length(list.name) < 30) {
mydata.names.grob <- textGrob(list.name, x = gbl.var$equidis.pos, y = unit(-8, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 1))), just=c("left"), name="mydata.names")
if(config.var$disp.color.ref) {
#Ref
mydata.names.grob.ref <- textGrob(name.ref, x = gbl.var$equidis.pos[gbl.var$mydata.ref.pos], y = unit(-8, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 1) ),col="darkorchid1"), just=c("left"), name="mydata.names.ref")
}
} else {
mydata.names.grob <- textGrob(list.name, x = gbl.var$equidis.pos, y = unit(-15, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 1) )), just=c("left"), name="mydata.names")
if(config.var$disp.color.ref) {
#Ref
mydata.names.grob.ref <- textGrob(name.ref, x = gbl.var$equidis.pos[gbl.var$mydata.ref.pos], y = unit(-15, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 1)),col="darkorchid1"), just=c("left"), name="mydata.names.ref")
}
}
} else if (config.var$image.size == 7) {
if( length(gbl.var$sorted.mydata.names) < 30) {
mydata.names.grob <- textGrob(list.name, x = gbl.var$equidis.pos, y = unit(-8, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 2) )), just=c("left"), name="mydata.names")
if(config.var$disp.color.ref) {
#Ref
mydata.names.grob.ref <- textGrob(name.ref, x = gbl.var$equidis.pos[gbl.var$mydata.ref.pos], y = unit(-8, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize =((gbl.var$font.size - 2)),col="darkorchid1"), just=c("left"), name="mydata.names.ref")
}
}else {
mydata.names.grob <- textGrob(list.name, x = gbl.var$equidis.pos, y = unit(-15, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 2))), just=c("left"), name="mydata.names")
if(config.var$disp.color.ref) {
#Ref
mydata.names.grob.ref <- textGrob(name.ref, x = gbl.var$equidis.pos[gbl.var$mydata.ref.pos], y = unit(-15, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize =((gbl.var$font.size - 2)),col="darkorchid1"), just=c("left"), name="mydata.names.ref")
}
}
}
if(config.var$disp.mydata.names) {
grid.draw(mydata.names.grob)
if(config.var$disp.color.ref) {
grid.draw(mydata.names.grob.ref)
}
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.GRID.MYDATA.NAMES\n")
}
#------------------------------------------------------
#------------- SET PARAMETER DRAW (color, symbole)-----
#------------- CREATE COLOR BAR ------------------------
create.color.bar <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE COLOR BAR\n")
cormatrix.matrix.ref <- gbl.var$ref
cormatrix.matrix <- gbl.var$cormatrix.data
cormatrix.pvalue.matrix <- gbl.var$cormatrix.pvalue.data.full
if(config.var$use.colors) {
if(config.var$cormatrix.color.scheme == "heat") {
cormatrix.colors <- heat.colors(gbl.var$palette.size)
} else if(config.var$cormatrix.color.scheme == "cm") {
cormatrix.colors <- cm.colors(gbl.var$palette.size)
} else if(config.var$cormatrix.color.scheme == "custom") {
if(!is.null(config.var$palette.file)) {
tmp.colors <- read.table(config.var$palette.file, as.is=TRUE, header=FALSE, blank.lines.skip = TRUE, fill=TRUE)
gbl.var$palette.size <- length(tmp.colors$V1)
custom.colors <- paste("#", tmp.colors$V1, sep="")
cormatrix.colors <- rev(custom.colors)
}
else {
dev.off()
stop("palette.file must be specified\n")
}
}
else if(config.var$cormatrix.color.scheme == "topo") {
cormatrix.colors <- topo.colors(gbl.var$palette.size)
}
else if(config.var$cormatrix.color.scheme == "gray") {
cormatrix.colors <- gray.colors(gbl.var$palette.size)
} else if(config.var$cormatrix.color.scheme == "bluetored"){
cormatrix.colors <- colorRampPalette(c("blue","red"))(gbl.var$palette.size)
} else if(config.var$cormatrix.color.scheme == "bluewhitered"){
cormatrix.colors <- colorRampPalette(c("blue","white","red"))(gbl.var$palette.size)
}
else {
dev.off()
stop("Invalid color scheme: ", config.var$cormatrix.color.scheme, "\n")
}
}
else {
cormatrix.colors <- gray.colors(gbl.var$palette.size)
}
#color.bar.colors <- c(rep(NA, gbl.var$palette.size), cormatrix.colors[gbl.var$palette.size:1])
color.bar.colors <- c(rep(NA, gbl.var$palette.size), cormatrix.colors[gbl.var$palette.size:1])
#DEBUG STATEMENT
# if (config.var$verbose) cat("color.bar.colors ", color.bar.colors, "\n")
#height=0.125
color.bar <- rectGrob(x=rep(seq(1:gbl.var$palette.size)/gbl.var$palette.size, 2),
y=rep(seq(1:2)/2, each=gbl.var$palette.size),
width=(1/gbl.var$palette.size),
height=0.075,
just=c("right", "top"),
gp=gpar(col=NULL,
fill=color.bar.colors,
cex = (gbl.var$cex.factor + 0.2),
lty="blank"),
name = "color.bar")
# color.bar.labels <- textGrob(paste(c(-1,-0.6,-0.2,0.2,0.6,1)), x=0.2*0:5, y=0.8, gp=gpar(fontsize = gbl.var$font.size), name="color.bar.labels")
color.bar.labels <- textGrob(paste(c(1,0.6,0.2,-0.2,-0.6,-1)), x=0.2*0:5, y=0.8, gp=gpar(fontsize = (gbl.var$font.size *config.var$font.factor)), name="color.bar.labels")
cormatrix.key.vp <- viewport(x=0.2, y=-0.03, width = 0.25, height = 0.25)
cormatrix.key <- gTree(children=gList(color.bar, color.bar.labels), name = "cormatrix.key", vp=cormatrix.key.vp)
if(config.var$disp.phys.dist) {
if(gbl.var$total.dist > 1000) {
map.label.text.distance <- paste("Physical Distance: ", round(gbl.var$total.dist/1000, 1), " kb", sep="")
} else {
map.label.text.distance <- paste("Physical Distance: ", gbl.var$total.dist, " bases", sep="")
}
} else {
map.label.text.distance <- " "
}
if (config.var$cormatrix.method == "spearman") {
map.label.text.ldtype <- "Correlation Matrix Map Type: Spearman"
} else if (config.var$cormatrix.method == "pearson") {
map.label.text.ldtype <- "Correlation Matrix Map Type: Pearson"
} else if (config.var$cormatrix.method == "kendall") {
map.label.text.ldtype <- "Correlation Matrix Map Type: Kendall"
} else {
dev.off()
stop("Invalid CORMATRIX metric : ", config.var$cormatrix.method, "\n")
}
map.label.distance <- textGrob(map.label.text.distance,
x = 0.2,
y = 0.1425,
just=("center"),
gp = gpar(fontsize = (gbl.var$font.size * config.var$font.factor)),
name="map.label.distance")
map.label.ldtype <- textGrob(map.label.text.ldtype,
x = 0.2,
y = 0.11150,
just=("center"),
gp = gpar(fontsize = (gbl.var$font.size *config.var$font.factor)),
name="map.label.ldtype")
matrix.rows <- dim(cormatrix.matrix)[1]
matrix.cols <- dim(cormatrix.matrix)[2]
intervals<-2/(length(cormatrix.colors))
color.intervals <- seq(-1,1,by=intervals)
# cat(length(color.intervals),"\n")
# cat(length(cormatrix.colors),"\n")
#Create the color of correlation matrix
tmp.color.cut <- as.character(cut(cormatrix.matrix, color.intervals, labels=as.character(cormatrix.colors)))
color.cut.ref <- as.character(cut(cormatrix.matrix.ref, color.intervals, labels=as.character(cormatrix.colors)))
tmp.vector <- NULL
for(i in seq(0, matrix.rows - 1)) {
for(j in seq(matrix.rows, 1, by =-1)) {
tmp.vector <- c(tmp.vector, (matrix.rows*j-i))
}
}
#List of case to put white
blank.vector <- NULL
for(i in seq(0, matrix.rows -1)) {
for(j in seq(1, (matrix.rows-i + 1), by =1)) {
blank.vector <- c(blank.vector, (matrix.rows*j-i))
}
}
color.cut <- rep(NULL, matrix.rows^2)
for(i in 1:matrix.rows^2) {
if(config.var$cormatrix.format == "raw" |
config.var$cormatrix.format == "raw_rev" |
config.var$cormatrix.format == "DTR_RAW") {
#Define row and colunm number from i
r <- (as.integer(i/matrix.rows))
r.tmp <- i/matrix.rows
if(r.tmp%%1==0){
# if (config.var$verbose) cat("integer")
} else {
r <- r + 1
}
c <- i - (r-1)*matrix.rows
v<- cormatrix.pvalue.matrix[r,c]
if (config.var$verbose) cat ("Pvalue in ",i,":",r,"-",c," is ",v,"\n")
if( cormatrix.pvalue.matrix[r,c] <= config.var$cormatrix.sig.level) {
color.cut[i] <- tmp.color.cut[tmp.vector[i]]
} else if(tmp.vector[i] %in% blank.vector){
#it is blank value
color.cut[i] <- tmp.color.cut[tmp.vector[i]]
} else {
color.cut[i] <- "ghostwhite"
}
} else {
color.cut[i] <- tmp.color.cut[tmp.vector[i]]
}
}
if (config.var$verbose) cat("FINISH CREATE.COLOR.BAR\n")
return(list(color.cut = color.cut, color.cut.ref =color.cut.ref, cormatrix.key = cormatrix.key, map.label.ldtype = map.label.ldtype, map.label.distance = map.label.distance))
}
#-------------------CREATE LIST of COLOR----------------------------
create.color.list <- function(config.var,gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.color.list\n")
if(config.var$use.colors) {
tmp.color.list <- c("red", "blue", "green", "black", "orange")
}
else {
tmp.color.list <- c("grey0", "grey20", "grey40", "grey60", "grey80")
}
if(!is.null(config.var$color.list)) {
split.tmp.color.list <- strsplit(config.var$color.list, ",")
if(gbl.var$mydata.samples != length(split.tmp.color.list[[1]])) {
dev.off()
stop("The color list must have ", gbl.var$mydata.samples, " colors separated by commas without spaces.\n")
}
} else {
if(gbl.var$mydata.samples <= 5) {
split.tmp.color.list <- list(head(tmp.color.list, gbl.var$mydata.samples))
} else {
dev.off()
stop("coMET includes a default set of colors for 5 samples. For more samples, please specify color.list\n")
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.color.list\n")
return(split.tmp.color.list)
}
#-------------------CREATE LIST of COLOR FOR LARGE DATA----------------------------
create.color.list.large <- function(config.var,gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.color.list.large\n")
if(config.var$use.colors) {
tmp.color.list <- c("red", "blue", "green", "black", "orange")
}
else {
tmp.color.list <- c("grey0", "grey20", "grey40", "grey60", "grey80")
}
if(!is.null(config.var$color.list.large)) {
large.split.tmp.color.list <- strsplit(config.var$color.list.large, ",")
if(gbl.var$large.mydata.samples != length(large.split.tmp.color.list[[1]])) {
dev.off()
stop("The color list must have ", gbl.var$large.mydata.samples, " colors separated by commas without spaces.\n")
}
} else {
if(gbl.var$large.mydata.samples <= 5) {
large.split.tmp.color.list <- list(head(tmp.color.list, gbl.var$large.mydata.samples))
} else {
dev.off()
stop("coMET includes a default set of colors for 5 samples. For more samples, please specify color.list.large\n")
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.color.list.large\n")
return(large.split.tmp.color.list)
}
#-------------------CREATE LIST of SYMBOLE----------------------------
create.symbol.list <- function(config.var, split.color.list, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.SYMBOL.LIST\n")
tmp.symbol.list <- c("circle-fill", "square-fill", "diamond-fill", "triangle-fill", "circle")
if(!is.na(config.var$symbols)) {
split.tmp.symbol.list <- strsplit(config.var$symbols, ",")
if(gbl.var$mydata.samples != length(split.tmp.symbol.list[[1]])) {
dev.off()
stop("The symbol list must have ", gbl.var$mydata.samples, " symbol(s) separated by commas without spaces.\n")
}
} else {
if(gbl.var$mydata.samples <= 5) {
split.tmp.symbol.list <- list(head(tmp.symbol.list, gbl.var$mydata.samples))
} else {
dev.off()
stop("coMET includes a default set of colors for 5 samples. For more samples, please specify symbols\n")
}
}
split.symbol.list <- NULL
for(i in 1:gbl.var$mydata.samples) {
if(any(grep("circle", split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
split.symbol.list <- c(split.symbol.list, 21)
} else if(any(grep("square", split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
split.symbol.list <- c(split.symbol.list, 22)
} else if(any(grep("diamond", split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
split.symbol.list <- c(split.symbol.list, 23)
} else if(any(grep("triangle", split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
split.symbol.list <- c(split.symbol.list, 24)
} else if(any(grep("NA", split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
split.symbol.list <- c(split.symbol.list, NA)
} else {
dev.off()
stop("Unknown symbol: ", split.tmp.symbol.list[[1]][i], "\n")
}
}
split.fill.list <- list(rep("white", gbl.var$mydata.samples))
fill.pos <- grep("fill", split.tmp.symbol.list[[1]], ignore.case = TRUE)
#DEBUG STATEMENT
# if (config.var$verbose) cat("fill.pos ", fill.pos, "\n")
split.fill.list[[1]][fill.pos] <- split.color.list[[1]][fill.pos]
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.SYMBOL.LIST\n")
return(list(split.symbol.list = split.symbol.list, split.fill.list = split.fill.list))
}
#-------------------CREATE LIST of SYMBOLE FOR LARGE DATA----------------------------
create.symbol.list.large <- function(config.var, large.split.color.list, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.SYMBOL.LIST.large\n")
large.tmp.symbol.list <- c("circle-fill", "square-fill", "diamond-fill", "triangle-fill", "circle")
if(!is.na(config.var$symbols.large)) {
large.split.tmp.symbol.list <- strsplit(config.var$symbols.large, ",")
if(gbl.var$large.mydata.samples != length(large.split.tmp.symbol.list[[1]])) {
dev.off()
stop("The symbol list must have ", gbl.var$large.mydata.samples, " symbol(s) separated by commas without spaces.\n")
}
} else {
if(gbl.var$large.mydata.samples <= 5) {
large.split.tmp.symbol.list <- list(head(large.tmp.symbol.list, gbl.var$large.mydata.samples))
} else {
dev.off()
stop("coMET includes a default set of colors for 5 samples. For more samples, please specify symbols\n")
}
}
large.split.symbol.list <- NULL
for(i in 1:gbl.var$large.mydata.samples) {
if(any(grep("circle", large.split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
large.split.symbol.list <- c(large.split.symbol.list, 21)
} else if(any(grep("square", large.split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
large.split.symbol.list <- c(large.split.symbol.list, 22)
} else if(any(grep("diamond", large.split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
large.split.symbol.list <- c(large.split.symbol.list, 23)
} else if(any(grep("triangle", large.split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
large.split.symbol.list <- c(large.split.symbol.list, 24)
} else if(any(grep("NA", large.split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
large.split.symbol.list <- c(large.split.symbol.list, NA)
} else {
dev.off()
stop("Unknown symbol: ", large.split.tmp.symbol.list[[1]][i], "\n")
}
}
large.split.fill.list <- list(rep("white", gbl.var$large.mydata.samples))
large.fill.pos <- grep("fill", large.split.tmp.symbol.list[[1]], ignore.case = TRUE)
#DEBUG STATEMENT
# if (config.var$verbose) cat("large.fill.pos ", large.fill.pos, "\n")
large.split.fill.list[[1]][large.fill.pos] <- large.split.color.list[[1]][large.fill.pos]
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.SYMBOL.LIST.large\n")
return(list(large.split.symbol.list = large.split.symbol.list, large.split.fill.list = large.split.fill.list))
}
#-------------------DRAW GENES NAMES for WEB PAGE----------------------------
draw.name.genes.web <- function(config.var,gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.NAME.GENES.WEB\n")
#DEBUG STATEMENT
# if (config.var$verbose) cat("gbl.var$font.size ", gbl.var$font.size, "\n")
popViewport()
top.vp <- gbl.var$top.vp
gene.name.vp.cormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 4,
layout.pos.col = 3,
just=c("left", "top"),
name = "gene.name.vp.cormatrixmap")
gene.name.vp.nocormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 5,
layout.pos.col = 3,
just=c("left", "top"),
name = "gene.namen.vp.nocormatrixmap")
if(config.var$disp.cormatrixmap) {
pushViewport(vpTree(top.vp, vpList(gene.name.vp.cormatrixmap)))
gene.name.vp <- gene.name.vp.cormatrixmap
}
else {
pushViewport(vpTree(top.vp, vpList(gene.name.vp.nocormatrixmap)))
gene.name.vp <- gene.name.vp.nocormatrixmap
}
#-------------------NAME of GENES BEGINS-----------------------
name.genes <- genesName_ENSEMBL(config.var$genome,gbl.var$mydata.chr,gbl.var$min.x,gbl.var$max.x,config.var$dataset.gene)
legend.name.genes.list <- NULL
if( !is.null(name.genes)) {
if(nrow(name.genes) <= 10) {
#All name.genes
# if (config.var$verbose) cat("All name.genes \n")
for(i in 1:nrow(name.genes)) {
label.text <- name.genes[i,2]
# if (config.var$verbose) cat("Gene",i,":", label.text,"\n")
#Ensure that labels do not overlap by moving them
y.pos <- 1.8 - 0.3 * ( i - 1)
x.pos <- 0.75
label.name.genes.text <- textGrob(label.text,
x = x.pos,
y = y.pos,
just=("left"),
gp = gpar(fontsize = ((gbl.var$font.size * 0.7 )),fontface = "bold"))
legend.name.genes.list[[(length(legend.name.genes.list) + 1)]] <- label.name.genes.text
}
class(legend.name.genes.list) <- c("gList")
legend.glist.name.genes <- legend.name.genes.list
# just=c("left", "top"),
legend.name.genes <- gTree(children=legend.glist.name.genes,
vp=gene.name.vp,
name="legend.gene.name")
grid.draw(legend.name.genes)
}
popViewport()
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.NAME.GENES.WEB\n")
return(gbl.var)
}
#-------------------DRAW NAMES OF TRACKS for WEB PAGE----------------------------
draw.name.tracks.web <- function(config.var,gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.NAME.TRACKS.WEB\n")
#DEBUG STATEMENT
# if (config.var$verbose) cat("gbl.var$font.size ", gbl.var$font.size, "\n")
popViewport()
top.vp <- gbl.var$top.vp
name.tracks.vp.cormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 4,
layout.pos.col = 1,
name = "name.tracks.vp.cormatrixmap")
name.tracks.vp.nocormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 5,
layout.pos.col = 1,
name = "name.tracks.vp.nocormatrixmap")
name.tracks.vp.cormatrixmap.nopval <- viewport(height = 1,
width = 1,
layout.pos.row = 3,
layout.pos.col = 1,
name = "name.tracks.vp.nocormatrixmap.nopval")
if(config.var$disp.cormatrixmap) {
if(config.var$disp.pvalueplot) {
pushViewport(vpTree(top.vp, vpList(name.tracks.vp.cormatrixmap)))
name.tracks.vp <- name.tracks.vp.cormatrixmap
} else {
pushViewport(vpTree(top.vp, vpList(name.tracks.vp.cormatrixmap.nopval)))
name.tracks.vp <- name.tracks.vp.cormatrixmap.nopval
}
}
else {
pushViewport(vpTree(top.vp, vpList(name.tracks.vp.nocormatrixmap)))
name.tracks.vp <- name.tracks.vp.nocormatrixmap
}
#-------------------NAME of TRACKS BEGINS-----------------------
legend.tracks.list <- NULL
y.label.pos <- c(1.25,0, -0.35,-0.85,-1.15,-1.45,-1.75)
num.tracks <- 1
if(config.var$image.size == 3.5) {
#All tracks cf order define via create.tracks.web
# if (config.var$verbose) cat("All tracks \n")
y.label.pos <- c(1.25,0.15, -0.25,-0.75,-1.25,-1.65,-1.95)
} else if(config.var$image.size == 7) {
y.label.pos <- c(1.25,0.30, -0.1, -0.7, -1.3, -1.7, -2.1)
}
#--- GENES ENSEMBL
if(has.key("geneENSEMBL", gbl.var$split.list.tracks)) {
label.tracks.text.ensembl <- textGrob("ENSEMBL Genes",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size*0.75*config.var$font.factor),
fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.ensembl
num.tracks <- num.tracks + 1
}
if(has.key("transcriptENSEMBL", gbl.var$split.list.tracks)) {
label.tracks.text.ensembl <- textGrob("ENSEMBL Transcripts",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size*0.75*config.var$font.factor),
fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.ensembl
num.tracks <- num.tracks + 1
}
#--- genes UCSC
if(has.key("genesUCSC",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("genes UCSC",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- xenogenes UCSC
if(has.key("xenogenesUCSC",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("xeno genes UCSC",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- CG Island
if(has.key("CGI",gbl.var$split.list.tracks)) {
label.tracks.text.cgisland <- textGrob("CG Island",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor ),
fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.cgisland
num.tracks <- num.tracks + 1
}
#--- ChromatinHMM
if(has.key("ChromHMM",gbl.var$split.list.tracks)) {
label.tracks.text.chromatinhmm <- textGrob("Broad ChromHMM",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),
fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.chromatinhmm
num.tracks <- num.tracks + 1
}
#--- DNAse
if(has.key("DNAse",gbl.var$split.list.tracks)) {
label.tracks.text.dnase <- textGrob("DNase Clusters",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.dnase
num.tracks <- num.tracks + 1
}
#--- Regulation ENSEMBL
if(has.key("RegENSEMBL",gbl.var$split.list.tracks)) {
label.tracks.text.reg <- textGrob("Regulation ENSEMBL",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.reg
num.tracks <- num.tracks + 1
}
#--- SNP
if(has.key("SNP",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("SNP UCSC",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- SNPstoma
if(has.key("SNPstoma",gbl.var$split.list.tracks)) {
label.tracks.text.chromatinhmm <- textGrob("SNP stomatic cells",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.chromatinhmm
num.tracks <- num.tracks + 1
}
#--- SNPstru
if(has.key("SNPstru",gbl.var$split.list.tracks)) {
label.tracks.text.dnase <- textGrob("structural SNP",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.dnase
num.tracks <- num.tracks + 1
}
#--- SNPstrustoma
if(has.key("SNPstrustoma",gbl.var$split.list.tracks)) {
label.tracks.text.dnase <- textGrob(" stomatic stuctural SNP",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.dnase
num.tracks <- num.tracks + 1
}
#--- ISCA
if(has.key("ISCA",gbl.var$split.list.tracks)) {
label.tracks.text.reg <- textGrob("ISCA",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.reg
num.tracks <- num.tracks + 1
}
#--- COSMIC
if(has.key("COSMIC",gbl.var$split.list.tracks)) {
label.tracks.text.reg <- textGrob("COSMIC",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.reg
num.tracks <- num.tracks + 1
}
#--- GAD
if(has.key("GAD",gbl.var$split.list.tracks)) {
label.tracks.text.reg <- textGrob("GAD",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.reg
num.tracks <- num.tracks + 1
}
#--- ClinVar
if(has.key("ClinVar",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("ClinVar",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- GeneReviews
if(has.key("GeneReviews",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("GeneReviews",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- GWAS
if(has.key("GWAS",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("GWAS",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- ClinVarCNV
if(has.key("ClinVarCNV",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("ClinVarCNV",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- GC content
if(has.key("GCcontent",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("GC content",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- Repeat Element
if(has.key("RepeatElt",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("Repeat elements",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
class(legend.tracks.list) <- c("gList")
legend.glist.tracks <- legend.tracks.list
# just=c("left", "top"),
legend.tracks <- gTree(children=legend.glist.tracks,
vp=name.tracks.vp,
name="legend.tracks")
grid.draw(legend.tracks)
popViewport()
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.NAME.TRACKS.WEB\n")
return(gbl.var)
}
#------------------ CREATE TRACKS for USER ------------------------------
create.tracks.user <- function(config.var,gbl.var){
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.TRACKS.USER\n")
if(!is.null(config.var$biofeat.user.file)){
split.biofeature.data.user.file <- gbl.var$split.biofeature.data.user.file
split.biofeature.data.user.type <- gbl.var$split.biofeature.data.user.type
split.biofeature.data.user.type.plot <- gbl.var$split.biofeature.data.user.type.plot
num.data=0
listtracks_user <- list()
track.biofeat <- NULL
cur.biofeat <- 0
for(i in 1:length(split.biofeature.data.user.file[[1]])) {
cur.biofeat <- i
cur.biofeat.data <- split.biofeature.data.user.file[[1]][i]
cur.biofeat.type <- split.biofeature.data.user.type[[1]][i]
if(cur.biofeat.type == "GeneRegion"){
track.biofeat <- GeneRegionTrack(range=cur.biofeat.data, genome=config.var$genome, chromosome=gbl.var$mydata.chr)
}else if (cur.biofeat.type == "Annotation") {
track.biofeat <- AnnotationTrack(range=cur.biofeat.data, genome=config.var$genome, chromosome=gbl.var$mydata.chr)
}else if (cur.biofeat.type == "DATA") {
num.data <- num.data + 1
cur.biofeat.type.plot <- split.biofeature.data.user.type.plot[[1]][num.data]
track.biofeat <- DataTrack(range=cur.biofeat.data, genome=config.var$genome, type=cur.biofeat.type.plot, chromosome=gbl.var$mydata.chr)
}else {
dev.off()
stop("TYPE of TRACK UNKNOWN \n")
}
if (cur.biofeat == 0){
listtracks_user=list(track.biofeat)
}else{
listtracks_user = c(listtracks_user, track.biofeat)
}
}
gbl.var$listtracks_user <- c(listtracks_user)
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.TRACKS.USER\n")
return(gbl.var)
}
#-------------------CREATE TRACKS for WEB PAGE----------------------------
create.tracks.web <- function(config.var,gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.TRACKS.WEB\n")
listtracks_gviz <-list()
# if (config.var$verbose) cat("test",is.hash(gbl.var$split.list.tracks))
#---- genome Axis
if(has.key("genomeAxis", gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw genomeAxis\n")
gtrack <- GenomeAxisTrack()
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(gtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,gtrack)
}
}
#--- GENES ENSEMBL
if(has.key("geneENSEMBL", gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw geneENSEMBL\n")
ENSEMBLtrack <- genes_ENSEMBL(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x,showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(ENSEMBLtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,ENSEMBLtrack)
}
}
#--- transcript ENSEMBL
if(has.key("transcriptENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw transcriptENSEMBL\n")
tENSEMBLtrack <- transcript_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x,showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(tENSEMBLtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,tENSEMBLtrack)
}
}
#--- Known gene UCSC
if(has.key("genesUCSC",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw genesUCSC\n")
dnasetrack<-knownGenes_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,
gbl.var$max.x,showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(dnasetrack)
} else {
listtracks_gviz <- c(listtracks_gviz,dnasetrack)
}
}
#--- ref gene UCSC
if(has.key("refgenesUCSC",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw ref genes UCSC\n")
refGenestrack<-refGenes_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x,
IdType = "Ref", showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(refGenestrack)
} else {
listtracks_gviz <- c(listtracks_gviz,refGenestrack)
}
}
#------ xeno ref
if(has.key("xenogenesUCSC",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw xenogenesUCSC\n")
gctrack <-xenorefGenes_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,
gbl.var$max.x,showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(gctrack)
} else {
listtracks_gviz <- c(listtracks_gviz,gctrack)
}
}
#--- CG Island
if(has.key("CGI",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw CGI\n")
cgitrack<-cpgIslands_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(cgitrack)
} else {
listtracks_gviz <- c(listtracks_gviz,cgitrack)
}
}
#--- ChromatinHMM
if(has.key("ChromHMM",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw ChromHMM\n")
chromatintrack <- chromatinHMMAll_UCSC(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x,gbl.var$mySession,
color= 'coMET',
config.var$pattern.regulation)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(chromatintrack)
} else {
listtracks_gviz <- c(listtracks_gviz,chromatintrack)
}
}
#--- Broad Histone
if(has.key("BroadHistone",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw BroadHistone\n")
chromatintrack <- HistoneAll_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x,
gbl.var$mySession,track.name="Broad histone",
pattern=config.var$pattern.regulation)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(chromatintrack)
} else {
listtracks_gviz <- c(listtracks_gviz,chromatintrack)
}
}
#--- DNAse
if(has.key("DNAse",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw DNAse\n")
dnasetrack<-DNAse_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,
gbl.var$max.x,gbl.var$mySession)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(dnasetrack)
} else {
listtracks_gviz <- c(listtracks_gviz,dnasetrack)
}
}
#---- Regulation (hg19)
if(has.key("RegENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw RegENSEMBL\n")
regtrack<-regulationBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(regtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,regtrack)
}
}
#---- BindingMotifENSEMBL
if(has.key("BindingMotifENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw BindingMotifENSEMBL\n")
BMtrack<-bindingMotifsBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(BMtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,BMtrack)
}
}
#---- regulatoryFeaturesENSEMBL
if(has.key("otherRegulatoryENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw otherRegulatoryENSEMBL\n")
ORtrack<-otherRegulatoryRegionsBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(ORtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,ORtrack)
}
}
#---- regulatoryFeaturesENSEMBL
if(has.key("regulatoryEvidenceENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw regulatoryFeaturesENSEMBL\n")
REtrack<-regulatoryEvidenceBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(REtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,REtrack)
}
}
#---- regulatoryFeaturesENSEMBL
if(has.key("regulatoryFeaturesENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw regulatoryFeaturesENSEMBL\n")
RFtrack<-regulatoryFeaturesBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(RFtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,RFtrack)
}
}
#---- regulatorySegmeENSEMBL
if(has.key("regulatorySegmeENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw regulatorySegmeENSEMBL\n")
RStrack<-regulatorySegmentsBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(RStrack)
} else {
listtracks_gviz <- c(listtracks_gviz,RStrack)
}
}
#---- miRNA
if(has.key("miRNAENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw miRNAENSEMBL\n")
mirnatrack<-miRNATargetRegionsBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,
gbl.var$min.x,
gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(mirnatrack)
} else {
listtracks_gviz <- c(listtracks_gviz,mirnatrack)
}
}
#---- structural variation
if(has.key("SNPstru",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw SNPstru\n")
structrack<-structureBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x,"*",
config.var$DATASET.STRU)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(structrack)
} else {
listtracks_gviz <- c(listtracks_gviz,structrack)
}
}
#---- stomatic structural variation
if(has.key("SNPstrustoma",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw SNPstrustoma\n")
structrack<-structureBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x,"*",
config.var$DATASET.STRU.STOMA)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(structrack)
} else {
listtracks_gviz <- c(listtracks_gviz,structrack)
}
}
#---- SNP stomatic cell
if(has.key("SNPstoma",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw SNPstoma\n")
snpstomaENSEMBLtrack<-snpBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,gbl.var$max.x,
config.var$DATASET.SNP.STOMA,
title="Stomatic Short Variation")
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(snpstomaENSEMBLtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,snpstomaENSEMBLtrack)
}
}
#---- SNP
if(has.key("SNP",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw SNP\n")
snptrack <- snpLocations_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,
gbl.var$max.x,config.var$VERSION.DBSNP)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(snptrack)
} else {
listtracks_gviz <- c(listtracks_gviz,snptrack)
}
}
#------ Imprinted genes
if(has.key("ImprintedtissuesGenes",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw tissue-specific imprinted genes \n")
imprintedtrack <-imprintedGenes_GTEx(gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x, tissues="all",
classification="all",showId=FALSE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(imprintedtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,imprintedtrack)
}
}
#------ COSMIC
if(has.key("COSMIC",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw COSMIC\n")
cosmictrack <-COSMIC_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x,showId=FALSE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(cosmictrack)
} else {
listtracks_gviz <- c(listtracks_gviz,cosmictrack)
}
}
#------ GAD
if(has.key("GAD",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw GAD\n")
iscatrack <-GAD_UCSC(config.var$genome,gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x,showId=FALSE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(iscatrack)
} else {
listtracks_gviz <- c(listtracks_gviz,iscatrack)
}
}
#------ clinic Variant
if(has.key("ClinVar",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw ClinVar\n")
clinVariant<-ClinVarMain_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(clinVariant)
} else {
listtracks_gviz <- c(listtracks_gviz,clinVariant)
}
}
if(has.key("ClinVarCNV",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw ClinVarCNV\n")
clinCNV<-ClinVarCnv_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(clinCNV)
} else {
listtracks_gviz <- c(listtracks_gviz,clinCNV)
}
}
#------ GWAS Variant
if(has.key("GWAS",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw GWAS\n")
gwastrack <-GWAScatalog_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(gwastrack)
} else {
listtracks_gviz <- c(listtracks_gviz,gwastrack)
}
}
#------ GeneReviews
if(has.key("GeneReviews",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw GeneReviews\n")
geneRtrack <-GeneReviews_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(geneRtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,geneRtrack)
}
}
#------ GC content
if(has.key("GCcontent",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw GCcontent\n")
gctrack <-gcContent_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(gctrack)
} else {
listtracks_gviz <- c(listtracks_gviz,gctrack)
}
}
#------ Repeat element
if(has.key("RepeatElt",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw RepeatElt\n")
reptrack <-repeatMasker_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x,showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(reptrack)
} else {
listtracks_gviz <- c(listtracks_gviz,reptrack)
}
}
#------ Segmental duplication
if(has.key("SegDuplication",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw SegDuplication\n")
segDuptrack <-segmentalDups_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(segDuptrack)
} else {
listtracks_gviz <- c(listtracks_gviz,segDuptrack)
}
}
#------ BioUSER
if(!is.null(config.var$biofeat.user.file)){
if (config.var$verbose) cat("Draw BioUser\n")
if(length(gbl.var$listtracks_user) == 0) {
listtracks_gviz <- gbl.var$listtracks_user
} else {
listtracks_gviz <- c(listtracks_gviz,gbl.var$listtracks_user)
}
}
# if (config.var$zoom) {
# listtracks_gviz=c(list(tENSEMBLtrack,cgitrack),chromatintrack,dnasetrack,regtrack,snptrack)
# }else {
# listtracks_gviz=c(list(ENSEMBLtrack,cgitrack),chromatintrack,dnasetrack,regtrack,snptrack)
# }
gbl.var$listtracks_gviz <- listtracks_gviz
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.TRACKS.WEB\n")
return(gbl.var)
}
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R Package Documentation
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Defines functions create.tracks.web create.tracks.user draw.name.tracks.web draw.name.genes.web create.symbol.list.large create.symbol.list create.color.list.large create.color.list create.color.bar draw.plot.grid.mydata.names draw.legend draw.plot.cormatrix.plot draw.plot.grid.mydata.large draw.plot.grid.mydata draw.plot.mydata.ggbio draw.plot.annotation draw.plot.axis.data draw.plot.linesconnection draw.plot.grid.setup
Documented in create.color.bar create.color.list create.color.list.large create.symbol.list create.symbol.list.large create.tracks.user create.tracks.web draw.legend draw.name.genes.web draw.name.tracks.web draw.plot.annotation draw.plot.axis.data draw.plot.cormatrix.plot draw.plot.grid.mydata draw.plot.grid.mydata.large draw.plot.grid.mydata.names draw.plot.grid.setup draw.plot.linesconnection draw.plot.mydata.ggbio
##########################################################################
# This program is free software; you can redistribute it and/or modify
# it under the terms of the GNU General Public License as published by
# the Free Software Foundation; either version 2 of the License, or
# (at your option) any later version.
#
# This program is distributed in the hope that it will be useful,
# but WITHOUT ANY WARRANTY; without even the implied warranty of
# MERCHANTABILITY or FITNESS FOR A PARTICULAR PURPOSE. See the
# GNU General Public License for more details.
#
# You should have received a copy of the GNU General Public License
# along with this program; if not, write to the Free Software
##########################################################################
##########################################################################
# File: GeneralMethodComet.R
# Author: Tiphaine Martin
# Email: tiphaine.martin@kcl.ac.uk
# Purpose: coMET allows the display of p-values from association
# with a correlation heatmap.
# Version : 0.99.9
###########################################################################
#-------------------DRAW PLOT GRID----------------------------
draw.plot.grid.setup <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.GRID.SETUP\n")
#set y-axis initial value
if(config.var$disp.pval.threshold != -1) {
gbl.var$r.y[1] <- config.var$disp.pval.threshold
gbl.var$axis.y <- seq(floor(gbl.var$r.y[1]), max(gbl.var$axis.y))
} else {
gbl.var$r.y[1] <- 0
}
#-------------------VIEWPORT BEGINS------------------
#-------------------CORMATRIX VIEWPORT---------------------
# FOR CORMATRIX MAP
top.vp.cormatrixmap <- viewport(layout = grid.layout(7, 3, widths = c(0.18, 0.6875, 0.1325),
heights = c(.05, .025, .18, .24, .001, .5, .05)),
name = "top.vp.cormatrixmap")
top.vp.nocormatrixmap <- viewport(layout = grid.layout(6, 3, widths = c(0.18, 0.6875, 0.1325),,
heights = c(.05, .025, .42, .001, .5, .05)),
name = "top.vp.nocormatrixmap")
top.vp.cormatrixmap.nopval <- viewport(layout = grid.layout(6, 3, widths = c(0.18, 0.6875, 0.1325),
heights = c(.05, .025, .42, .001, .5, .05)),
name = "top.vp.cormatrixmap.nopval")
if(config.var$disp.pvalueplot){
if(config.var$disp.cormatrixmap) {
gbl.var$top.vp <- top.vp.cormatrixmap
}
else {
gbl.var$top.vp <- top.vp.nocormatrixmap
}
} else {
gbl.var$top.vp <- top.vp.cormatrixmap.nopval
}
#-------------------TITLE VIEWPORT---------------------
title.vp.cormatrixmap <- viewport(height = .8,
width = .8,
layout.pos.row = 1,
layout.pos.col = 2,
name = "title.vp.cormatrixmap")
title.vp.nocormatrixmap <- viewport(height = .8,
width = .8,
layout.pos.row = 1,
layout.pos.col = 2,
name = "title.vp.nocormatrixmap")
title.vp.cormatrixmap.nopval <- viewport(height = .8,
width = .8,
layout.pos.row = 1,
layout.pos.col = 2,
name = "title.vp.cormatrixmap.nopval")
if(config.var$disp.pvalueplot){
if(config.var$disp.cormatrixmap) {
pushViewport(vpTree(top.vp.cormatrixmap, vpList(title.vp.cormatrixmap )))
}
else {
pushViewport(vpTree(top.vp.nocormatrixmap, vpList(title.vp.nocormatrixmap )))
}
}else{
pushViewport(vpTree(top.vp.cormatrixmap.nopval, vpList(title.vp.cormatrixmap.nopval)))
}
image.title.text <- textGrob(config.var$image.title, x = 0.5, y = 0.5, just = c("center"),
default.units = "native", gp = gpar(fontsize = (gbl.var$font.size + 4 *config.var$font.factor), fontface = "bold.italic"))
image.title <- gTree(children=gList(image.title.text), vp=title.vp.cormatrixmap, name="image.title")
grid.draw(image.title)
#--------------------- PLOT CHROMOSOME ------------------------
popViewport()
chromosome.vp.cormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 2,
layout.pos.col = 2,
name = "chromosome.vp.cormatrixmap")
chromosome.vp.nocormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 2,
layout.pos.col = 2,
name = "chromosome.vp.nocormatrixmap")
chromosome.vp.cormatrixmap.nopval <- viewport(height = 1,
width = 1,
layout.pos.row = 2,
layout.pos.col = 2,
name = "chromosome.vp.cormatrixmap.nopval")
if(config.var$disp.pvalueplot){
if(config.var$disp.cormatrixmap) {
pushViewport(vpTree(top.vp.cormatrixmap, vpList(chromosome.vp.cormatrixmap )))
}
else {
pushViewport(vpTree(top.vp.nocormatrixmap, vpList(chromosome.vp.nocormatrixmap )))
}
} else {
pushViewport(vpTree(top.vp.cormatrixmap.nopval, vpList(chromosome.vp.cormatrixmap.nopval )))
}
itrack <- IdeogramTrack(genome=gbl.var$mydata.gen, chromosome=gbl.var$mydata.chr)
plotTracks(itrack,from=gbl.var$min.x,to=gbl.var$max.x,panel.only=TRUE, fontsize=config.var$fontsize.gviz,showBandId = TRUE, cex.bands = 0.5)
#-------------------CONNECTOR VIEWPORT---------------------
if(config.var$disp.cormatrixmap) {
if(config.var$disp.pvalueplot){
draw.plot.linesconnection(top.vp.cormatrixmap, config.var, gbl.var)
} else {
draw.plot.linesconnection(top.vp.cormatrixmap.nopval, config.var, gbl.var)
}
}
else {
popViewport()
}
#-------------------DATA VIEWPORT---------------------
if(config.var$disp.cormatrixmap & config.var$disp.pvalueplot) {
draw.plot.axis.data(top.vp.cormatrixmap, config.var, gbl.var)
}
else {
if(config.var$disp.cormatrixmap==FALSE & config.var$disp.pvalueplot){
draw.plot.axis.data(top.vp.nocormatrixmap, config.var, gbl.var)
} else {
popViewport()
}
}
#--------------------- POSITION of LEGEND PHYSICAL DISTANCE ------------------------
#display the physical distance on plots without LD maps
if(config.var$disp.phys.dist & !config.var$disp.cormatrixmap) {
if(gbl.var$total.dist > 1000) {
grid.text(paste("Physical Distance: ", round(gbl.var$total.dist/1000, 1), " kb", sep=""),
x = 0.5,
y = -1.15,
just = "center",
gp = gpar(fontsize = (gbl.var$font.size*config.var$font.factor)))
} else {
grid.text(paste("Physical Distance: ",
gbl.var$total.dist, " bases", sep=""),
x = 0.5, y = -1.15,
just = "center",
gp = gpar(fontsize = (gbl.var$font.size*config.var$font.factor)))
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.GRID.SETUP\n")
return(gbl.var)
}
#------------------- DRAW CONNECTOR -----------------------
draw.plot.linesconnection <- function(top.vp, config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.LINESCONNECTION\n")
popViewport()
# if (config.var$verbose) cat("gbl.var$r.x[1]", gbl.var$r.x[1], "\n")
# if (config.var$verbose) cat("gbl.var$r.y[2]", gbl.var$r.y[2], "\n")
# if (config.var$verbose) cat("gbl.var$axis.x[length(gbl.var$axis.x)]", gbl.var$axis.x[length(gbl.var$axis.x)], "\n")
# if (config.var$verbose) cat("gbl.var$axis.y[1]", gbl.var$axis.y[1], "\n")
#-------------------CONNECTOR VIEWPORT---------------------
connector.vp.cormatrixmap <- viewport(xscale = c(gbl.var$r.x[1], gbl.var$axis.x[length(gbl.var$axis.x)]),
yscale = c(gbl.var$axis.y[1], gbl.var$r.y[2]),
height = 0.8,
width = 0.8,
layout.pos.row = 5,
layout.pos.col = 2,
name = "data.vp.cormatrixmap")
connector.vp.cormatrixmap.nopval <- viewport(xscale = c(gbl.var$r.x[1], gbl.var$axis.x[length(gbl.var$axis.x)]),
yscale = c(gbl.var$axis.y[1], gbl.var$r.y[2]),
height = 0.8,
width = 0.8,
layout.pos.row = 4,
layout.pos.col = 2,
name = "data.vp.cormatrixmap.nopval")
if(config.var$disp.cormatrixmap) {
if(config.var$disp.pvalueplot) {
pushViewport(vpTree(top.vp, vpList(connector.vp.cormatrixmap)))
} else{
pushViewport(vpTree(top.vp, vpList(connector.vp.cormatrixmap.nopval)))
}
}
#-------------------AXIS BEGINS------------------
# if (config.var$verbose) cat("axis\n")
grid.lines(x = gbl.var$axis.x, y = 0, default.units = "native", gp = gpar(lty = 1, lwd = gbl.var$line.width))
#----------------------- X-AXIS --------------------------
# if (config.var$verbose) cat("x-axis\n")
if(config.var$disp.mult.lab.X) {
#Truncate the number of X-axis labels
if(length(gbl.var$axis.x) > 5) {
increment <- ceiling(length(gbl.var$axis.x) / 5)
axis.x.labels <- gbl.var$axis.x[seq(1, length(gbl.var$axis.x), by= increment)]
if(length(gbl.var$axis.x) %% 5 != 0) {
axis.x.labels <- c(axis.x.labels, gbl.var$axis.x[length(gbl.var$axis.x)])
}
}
}
else {
#Truncate the number of X-axis labels
if(length(gbl.var$axis.x) >= 2) {
axis.x.labels <- c(head(gbl.var$axis.x, 1), tail(gbl.var$axis.x, 1))
}
}
#DEBUG STATEMENT
# if (config.var$verbose) cat("cormatrixmap\n")
# if (config.var$verbose) cat("List",gbl.var$sorted.mydata.pos,"\n")
# if (config.var$verbose) cat("gbl.var$sorted.mydata.pos.zoom ", gbl.var$sorted.mydata.pos.zoom, "\n")
# if (config.var$verbose) cat("List zoom",gbl.var$sorted.mydata.pos.zoom,"\n")
grid.xaxis(at = axis.x.labels, label = FALSE, gp = gpar(cex = gbl.var$cex.factor), name = "axis.x.labels")
grid.xaxis(at = gbl.var$sorted.mydata.pos.zoom, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width))
grid.text(paste(axis.x.labels[1],"bp"), x = -0.025, y = -0.1, just = "right", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
grid.text(paste(axis.x.labels[2],"bp"), x = 1.015, y = -0.1, just = "left", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
if(config.var$disp.color.ref) {
#Color darkorchid1 the reference
grid.xaxis(at = gbl.var$mydata.ref.pos, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width,col="darkorchid1"))
}
#Remove trailing tick mark
grid.edit("axis.x.labels", gp = gpar(col = "white"))
#------------------ X-AXIS -----------------------
#-------------------EQUIDISPOS COORDINATE BEGINS-------------
# if (config.var$verbose) cat("equidistance\n")
gbl.var$equidis.pos <- NULL
#DEBUG STATEMENT
# if (config.var$verbose) cat("length(gbl.var$equidis.pos) ", length(gbl.var$equidis.pos), "\n")
# if (config.var$verbose) cat("length(gbl.var$mydata.num) ", length(gbl.var$mydata.pos), "\n")
gbl.var$mydata.num <- length(gbl.var$sorted.mydata.pos)
pos.increment <- (gbl.var$max.x - gbl.var$min.x) / gbl.var$mydata.num
#Attempt to center the MYDATA labels
start.pos <- gbl.var$min.x
for(i in 0:(gbl.var$mydata.num - 1)) {
gbl.var$equidis.pos <- c(gbl.var$equidis.pos, pos.increment * i + start.pos)
}
#-------------------CONNECTING LINES BEGINS-------------
if(config.var$connecting.lines.adj == -1) {
dev.off()
stop("connecting.lines.adj may not equal: -1")
}
tmp.correction.factor <- gbl.var$equidis.pos[1] * 10^(gbl.var$cur.exp - 9) * (1 + config.var$connecting.lines.adj)
#DEBUG STATEMENT
# if (config.var$verbose) cat("tmp.correction.factor ", tmp.correction.factor, "\n")
# if (config.var$verbose) cat("length(gbl.var$sorted.mydata.pos) ", length(gbl.var$sorted.mydata.pos), "\n")
# if (config.var$verbose) cat("length(gbl.var$equidis.pos) ", length(gbl.var$equidis.pos), "\n")
# if (config.var$verbose) cat("gbl.var$equidis.pos[1] ", gbl.var$equidis.pos[1], "\n")
# if (config.var$verbose) cat("gbl.var$cur.exp ", gbl.var$cur.exp, "\n")
# if (config.var$verbose) cat("config.var$connecting.lines.adj ", config.var$connecting.lines.adj, "\n")
length.sorted.mydata.pos.zoom <- length(gbl.var$sorted.mydata.pos.zoom)
if(config.var$image.size == 3.5) {
y.finish.pos <- rep(-0.9, length.sorted.mydata.pos.zoom * config.var$connecting.lines.factor)
} else if(config.var$image.size == 7) {
y.finish.pos <- rep(-1.8, length.sorted.mydata.pos.zoom * config.var$connecting.lines.factor)
}
#DEBUG STATEMENT
# if (config.var$verbose) cat("gbl.var$axis.y[1] ", gbl.var$axis.y[1], "\n")
# if (config.var$verbose) cat("y.finish.pos ", y.finish.pos, "\n")
if(config.var$connecting.lines.vert.adj != -1) {
y.start.pos <- config.var$connecting.lines.vert.adj
} else if (config.var$image.size == 3.5) {
y.start.pos <- -0.5
} else if (config.var$image.size == 7) {
y.start.pos <- -0.7
}else {
dev.off()
stop("Invalid image size: ", config.var$image.size, "\n")
}
# if (config.var$verbose) cat("BUG HERE \n")
# if (config.var$verbose) cat("BUGgg HERE \n")
x.finish.pos <- gbl.var$equidis.pos +
seq(1, length(gbl.var$equidis.pos) * abs(tmp.correction.factor), abs(tmp.correction.factor)) * config.var$connecting.lines.flex +
gbl.var$total.dist * config.var$connecting.lines.adj
#for reference sequence
ref.position <- which(gbl.var$sorted.mydata.pos == gbl.var$mydata.ref.pos)
x.finish.pos.zoom.ref <- x.finish.pos[ref.position]
#for region study
remove.position <- which(gbl.var$sorted.mydata.pos < gbl.var$min.x | gbl.var$sorted.mydata.pos > gbl.var$max.x)
if(length(remove.position) > 0){
x.finish.pos.zoom <- x.finish.pos[-remove.position]
} else {
x.finish.pos.zoom <- x.finish.pos
}
# if (config.var$verbose) cat("y.finish.pos ", y.finish.pos, "\n")
# if (config.var$verbose) cat("y.start.pos ", y.start.pos, "\n")
# if (config.var$verbose) cat("gbl.var$min.x ", gbl.var$min.x, "\n")
# if (config.var$verbose) cat("gbl.var$max.x ", gbl.var$max.x, "\n")
# if (config.var$verbose) cat("x.finish.pos", x.finish.pos, "\n")
# if (config.var$verbose) cat("remove.position", remove.position, "\n")
# if (config.var$verbose) cat("x.finish.pos.zoom ", x.finish.pos.zoom, "\n")
# if (config.var$verbose) cat("gbl.var$sorted.mydata.pos.zoom ", gbl.var$sorted.mydata.pos.zoom, "\n")
if(config.var$image.size == 3.5) {
connecting.lines <- segmentsGrob(x0 = x.finish.pos.zoom,
x1 = gbl.var$sorted.mydata.pos.zoom,
y0 = unit(y.finish.pos, "char"),
y1 = unit(y.start.pos, "char"),
default.units = "native",
gp = gpar(lwd = gbl.var$line.width))
######ref
if(config.var$disp.color.ref) {
######ref
if(gbl.var$mydata.ref.pos > gbl.var$min.x & gbl.var$mydata.ref.pos < gbl.var$max.x){
connecting.lines.ref <- segmentsGrob(x0 = x.finish.pos.zoom.ref,
x1 = gbl.var$mydata.ref.pos,
y0 = unit(y.finish.pos, "char"),
y1 = unit(y.start.pos,"char"),
default.units = "native",
gp = gpar(lwd = gbl.var$line.width,col="darkorchid1"))
}
}
} else if(config.var$image.size == 7) {
connecting.lines <- segmentsGrob(x0 = x.finish.pos.zoom,
x1 = gbl.var$sorted.mydata.pos.zoom,
y0 = unit(y.finish.pos, "char"),
y1 = unit(y.start.pos,"char"),
default.units = "native",
gp = gpar(lwd = gbl.var$line.width))
if(config.var$disp.color.ref) {
######ref
if(gbl.var$mydata.ref.pos > gbl.var$min.x & gbl.var$mydata.ref.pos < gbl.var$max.x){
connecting.lines.ref <- segmentsGrob(x0 = x.finish.pos.zoom.ref,
x1 = gbl.var$mydata.ref.pos,
y0 = unit(y.finish.pos, "char"),
y1 = unit(y.start.pos,"char"),
default.units = "native",
gp = gpar(lwd = gbl.var$line.width,col="darkorchid1"))
}
}
} else {
dev.off()
stop("Invalid image size: ", config.var$image.size, "\n")
}
# if (config.var$verbose) cat("BUGG HERE \n")
#DEBUG STATEMENT
# if (config.var$verbose) cat("y.finish.pos ", y.finish.pos, "\n")
# if (config.var$verbose) cat("connecting.lines ", is.null(connecting.lines), "\n")
# cat(is.null(connecting.lines), "\n")
# cat(x.finish.pos, "\n")
# cat(gbl.var$sorted.mydata.pos, "\n")
#----------------------- X-AXIS --------------------------
grid.lines(x = gbl.var$axis.x, y = 0, default.units = "native", gp = gpar(lty = 1, lwd = gbl.var$line.width, col="gray80"))
if(config.var$disp.connecting.lines) {
grid.draw(connecting.lines)
if(config.var$disp.color.ref) {
grid.draw(connecting.lines.ref)
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.LINECONNECTION\n")
}
#------------------- DRAW AXIS DATA -----------------------
draw.plot.axis.data <- function(top.vp, config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.AXIS.DATA\n")
popViewport()
#-------------------DATA VIEWPORT---------------------
data.vp.cormatrixmap <- viewport(xscale = c(gbl.var$r.x[1], gbl.var$axis.x[length(gbl.var$axis.x)]),
yscale = c(gbl.var$axis.y[1], gbl.var$r.y[2]),
height = 0.8,
width = 0.8,
layout.pos.row = 3,
layout.pos.col = 2,
name = "data.vp.cormatrixmap")
data.vp.nocormatrixmap <- viewport(xscale = c(gbl.var$r.x[1], gbl.var$axis.x[length(gbl.var$axis.x)]),
yscale = c(gbl.var$axis.y[1], gbl.var$r.y[2]),
height = .8,
width = .8,
layout.pos.row = 3,
layout.pos.col = 2,
name = "data.vp.nocormatrixmap")
if(config.var$disp.cormatrixmap) {
pushViewport(vpTree(top.vp, vpList(data.vp.cormatrixmap)))
}
else {
pushViewport(vpTree(top.vp, vpList(data.vp.nocormatrixmap)))
}
#-------------------AXIS BEGINS------------------
grid.lines(x = gbl.var$axis.x, y = gbl.var$axis.y[1], default.units = "native", gp = gpar(lty = "dashed", lwd = gbl.var$line.width))
#----------------------- X-AXIS --------------------------
if(config.var$disp.mult.lab.X) {
#Truncate the number of X-axis labels
if(length(gbl.var$axis.x) > 5) {
increment <- ceiling(length(gbl.var$axis.x) / 5)
axis.x.labels <- gbl.var$axis.x[seq(1, length(gbl.var$axis.x), by= increment)]
if(length(gbl.var$axis.x) %% 5 != 0) {
axis.x.labels <- c(axis.x.labels, gbl.var$axis.x[length(gbl.var$axis.x)])
}
}
}
else {
#Truncate the number of X-axis labels
if(length(gbl.var$axis.x) >= 2) {
axis.x.labels <- c(head(gbl.var$axis.x, 1), tail(gbl.var$axis.x, 1))
}
}
if(config.var$disp.cormatrixmap) {
if(! is.null(config.var$mydata.large.file)){
grid.xaxis(at = gbl.var$sorted.mydata.large.pos.zoom, label = FALSE, gp = gpar(col="grey", cex = gbl.var$cex.factor, lwd = gbl.var$line.width))
}
grid.xaxis(at = axis.x.labels, label = FALSE, gp = gpar(cex = gbl.var$cex.factor), name = "axis.x.labels")
grid.xaxis(at = gbl.var$sorted.mydata.pos.zoom, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width))
grid.text(paste(axis.x.labels[1],"bp"), x = -0.025, y = -0.1, just = "right", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
grid.text(paste(axis.x.labels[2],"bp"), x = 1.015, y = -0.1, just = "left", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
if(config.var$disp.color.ref) {
#Color red the reference
grid.xaxis(at = gbl.var$mydata.ref.pos, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width, col="darkorchid1"))
}
#Remove trailing tick mark
grid.edit("axis.x.labels", gp = gpar(col = "white"))
}
else {
if(! is.null(config.var$mydata.large.file)){
grid.xaxis(at = gbl.var$sorted.mydata.large.pos.zoom, label = FALSE, gp = gpar(col="grey", cex = gbl.var$cex.factor, lwd = gbl.var$line.width))
}
grid.xaxis(at = axis.x.labels, label = FALSE, gp = gpar(cex = gbl.var$cex.factor), name = "axis.x.labels")
grid.xaxis(at = gbl.var$sorted.mydata.pos.zoom, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width))
grid.text(paste(axis.x.labels[1],"bp"), x = -0.025, y = -0.09, just = "right", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
grid.text(paste(axis.x.labels[2],"bp"), x = 1.015, y = -0.09, just = "left", gp = gpar(fontsize = (gbl.var$font.size * 0.65 * config.var$font.factor)))
if(config.var$disp.color.ref) {
#Color red the reference
grid.xaxis(at = gbl.var$mydata.ref.pos, label = FALSE, gp = gpar(cex = gbl.var$cex.factor, lwd = gbl.var$line.width, col="darkorchid1"))
}
#Remove trailing tick mark
grid.edit("axis.x.labels", gp = gpar(col = "white"))
}
#------------------ X-AXIS -----------------------
#-------------------EQUIDISPOS COORDINATE BEGINS-------------
gbl.var$equidis.pos <- NULL
#DEBUG STATEMENT
# if (config.var$verbose) cat("length(gbl.var$equidis.pos) ", length(gbl.var$equidis.pos), "\n")
# if (config.var$verbose) cat("length(gbl.var$mydata.num) ", length(gbl.var$mydata.pos), "\n")
gbl.var$mydata.num <- length(gbl.var$sorted.mydata.pos)
if(config.var$disp.cormatrixmap) {
pos.increment <- (gbl.var$max.x - gbl.var$min.x) / gbl.var$mydata.num
#Attempt to center the MYDATA labels
start.pos <- gbl.var$min.x
for(i in 0:(gbl.var$mydata.num - 1)) {
gbl.var$equidis.pos <- c(gbl.var$equidis.pos, pos.increment * i + start.pos)
}
} else {
pos.increment <- (gbl.var$max.x - gbl.var$min.x) / gbl.var$mydata.num
#Attempt to center the MYDATA labels
start.pos <- gbl.var$min.x
for(i in 0:(gbl.var$mydata.num - 1)) {
gbl.var$equidis.pos <- c(gbl.var$equidis.pos, pos.increment * i + start.pos)
}
}
#----------------- Y-AXIS --------------------
if(config.var$lab.Y == "ln") {
if(config.var$disp.marker.lines) {
initial.abline <- 0.1
while(-log(initial.abline) < gbl.var$axis.y[1]) {
initial.abline <- initial.abline / 10
#DEBUG STATEMENT
if (config.var$verbose) cat("initial.abline 1", initial.abline, "\n")
}
while(-log(initial.abline) < max(gbl.var$axis.y)) {
#DEBUG STATEMENT
if (config.var$verbose) cat("initial.abline 2", initial.abline, "\n")
grid.lines(x = gbl.var$axis.x, y = -log(initial.abline), default.units = "native", gp = gpar(lty = "dashed", lwd = gbl.var$line.width, col="gainsboro"))
initial.abline <- initial.abline / 10
}
}
} else {
if(config.var$disp.marker.lines) {
initial.abline <- 0.1
while(-log10(initial.abline) < gbl.var$axis.y[1]) {
initial.abline <- initial.abline / 10
}
while(-log10(initial.abline) < max(gbl.var$axis.y)) {
grid.lines(x = gbl.var$axis.x, y = -log10(initial.abline), default.units = "native", gp = gpar(lty = "dashed", lwd = gbl.var$line.width, col="gainsboro"))
initial.abline <- initial.abline / 10
}
}
}
#----------- X-AXIS of THRESHOLD of pvalue
if(config.var$pval.threshold != 0 & config.var$pval.threshold > config.var$disp.pval.threshold){
grid.lines(x = gbl.var$axis.x, y = config.var$pval.threshold, default.units = "native", gp = gpar(lty = "dashed", lwd = gbl.var$line.width , col="red"))
}
#----------- X-AXIS of the second THRESHOLD of pvalue
if(config.var$pval.threshold.2 != 0 & config.var$pval.threshold.2 > config.var$disp.pval.threshold){
grid.lines(x = gbl.var$axis.x, y = config.var$pval.threshold.2, default.units = "native", gp = gpar(lty = "dashed", lwd = gbl.var$line.width , col="orange"))
}
#----------- X-AXIS of base
grid.lines(x = gbl.var$axis.x, y = gbl.var$axis.y[1], default.units = "native", gp = gpar(lwd = gbl.var$line.width))
grid.yaxis(at = gbl.var$axis.y, label = gbl.var$axis.y, gp = gpar(fontsize = gbl.var$font.size, lwd = gbl.var$line.width))
#----------- WRITE LABEL for Y-AXIS
if(config.var$lab.Y == "ln") {
grid.text("-ln(P-value)",
x = -0.1,
y = 0.5,
rot = 90,
gp = gpar(fontsize = (gbl.var$font.size * config.var$font.factor),
fontface = "bold"))
} else {
grid.text("-log10(P-value)",
x = -0.1,
y = 0.5,
rot = 90,
gp = gpar(fontsize = (gbl.var$font.size * config.var$font.factor),
fontface = "bold"))
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.AXIS.DATA\n")
}
#------------------- DRAW ANNOTATION -----------------------
draw.plot.annotation <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.ANNOTATION\n")
popViewport()
top.vp <- gbl.var$top.vp
annotation.vp.cormatrixmap <- viewport(height = 0.95,
width = 1,
layout.pos.row = 4,
layout.pos.col = 2,
name = "annotation.vp.cormatrixmap")
annotation.vp.nocormatrixmap <- viewport(height = 0.95,
width = 1,
layout.pos.row = 5,
layout.pos.col = 2,
name = "annotation.vp.nocormatrixmap")
annotation.vp.cormatrixmap.nopval <- viewport(height = 0.95,
width = 1,
layout.pos.row = 3,
layout.pos.col = 2,
name = "annotation.vp.cormatrixmap.nopval")
if(config.var$disp.cormatrixmap) {
if(config.var$disp.pvalueplot) {
pushViewport(vpTree(top.vp, vpList(annotation.vp.cormatrixmap)))
pushViewport(annotation.vp.cormatrixmap)
} else {
pushViewport(vpTree(top.vp, vpList(annotation.vp.cormatrixmap.nopval)))
pushViewport(annotation.vp.cormatrixmap.nopval)
}
}
else {
pushViewport(vpTree(top.vp, vpList(annotation.vp.nocormatrixmap)))
pushViewport(annotation.vp.nocormatrixmap)
}
size_gviz <- 0
if( ! is.null(gbl.var$listtracks_gviz)){
size_gviz <- length(gbl.var$listtracks_gviz) * 2
}
size_gviz_user <- 0
if(!is.null(config.var$biofeat.user.file)){
# gbl.var <- create.tracks.user(config.var,gbl.var)
size_gviz_user <- length(gbl.var$listtracks_user)
}
size_trackviewer <- 0
if( ! is.null(gbl.var$listtracks_trackviewer)){
size_trackviewer <- length(gbl.var$listtracks_trackviewer)
}
size_ggbio <- 0
if( ! is.null(gbl.var$listtracks_ggbio)){
size_ggbio <- length(gbl.var$listtracks_ggbio) * 4
}
total_tracks <- size_gviz + size_trackviewer + size_ggbio
if (config.var$verbose) cat("Number of track", total_tracks, "GVIZ", size_gviz,"\n")
annotvp <-viewport(layout=grid.layout(4, 1, heights=unit(c(size_gviz,size_ggbio,size_trackviewer,size_gviz_user),"null")),name = "annotviewport")
gvizviewport <- viewport(layout.pos.col = 1, layout.pos.row = 1, name = "gvizviewport")
ggbioviewport <- viewport(layout.pos.col = 1, layout.pos.row = 2, name = "ggbioviewport")
trackviewerviewport <- viewport(layout.pos.col = 1, layout.pos.row = 3, name = "trackviewerviewport")
gvizuserviewport <- viewport(layout.pos.col = 1, layout.pos.row = 4, name = "gvizuserviewport")
if(config.var$disp.cormatrixmap) {
if(config.var$disp.pvalueplot) {
pushViewport(vpTree(annotation.vp.cormatrixmap, vpList(gvizviewport, ggbioviewport, trackviewerviewport,gvizuserviewport)))
} else {
pushViewport(vpTree(annotation.vp.cormatrixmap.nopval, vpList(gvizviewport, ggbioviewport, trackviewerviewport,gvizuserviewport)))
}
}
else {
pushViewport(vpTree(annotation.vp.nocormatrixmap, vpList(gvizviewport, ggbioviewport, trackviewerviewport,gvizuserviewport)))
}
pushViewport(annotvp)
if(! (is.null(gbl.var$listtracks_gviz))){
seekViewport("annotviewport")
pushViewport(gvizviewport)
plotTracks(gbl.var$listtracks_gviz, from=gbl.var$min.x, to=gbl.var$max.x,panel.only=TRUE,add=TRUE, fontsize=config.var$fontsize.gviz)
}
if(! (is.null(gbl.var$listtracks_ggbio))){
seekViewport("annotviewport")
pushViewport(ggbioviewport)
l.g <- lapply(gbl.var$listtracks_ggbio, function(x){
ggplotGrob(x)
})
# grid.rect(gp=gpar(col="blue"))
grid.arrange(do.call(arrangeGrob, c(l.g, list(nrow = size_ggbio/4, ncol = 1))),newpage=FALSE)
#tracks(gbl.var$listtracks_ggbio)
}
if(! (is.null(gbl.var$listtracks_trackviewer))){
seekViewport("annotviewport")
pushViewport(trackviewerviewport)
viewTracks(trackList(gbl.var$listtracks_trackviewer),chromosome=gbl.var$mydata.chr,start=gbl.var$min.x, end=gbl.var$max.x,newpage=FALSE)
}
if(! (is.null(gbl.var$listtracks_user))){
seekViewport("annotviewport")
pushViewport(gvizuserviewport)
plotTracks(gbl.var$listtracks_user, from=gbl.var$min.x, to=gbl.var$max.x,panel.only=TRUE,add=TRUE, fontsize=config.var$fontsize.gviz)
}
popViewport()
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.ANNOTATION\n")
}
#------------------- DRAW DATA via GGBIO -----------------------
draw.plot.mydata.ggbio <- function(config.var, gbl.var,numfile) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.MYDATA\n")
split.mydata.file <- gbl.var$split.mydata.file
gbl.var <-read.file.mydata(split.mydata.file[[1]],config.var, gbl.var,numfile)
# if (config.var$verbose) cat("READ ",i," MYDATA file \n")
mydata.data <- gbl.var$mydata.data
mydata.pv <- log(mydata.data[,4])
startlist<-mydata.data[,3]
endlist<-mydata.data[,3]
id<-mydata.data[,1]
cprange<-GRanges(gbl.var$mydata.chr,IRanges(startlist,endlist))
# startlarge<-start-50000
# endlarge<-end+50000
cpidrange<-GRanges(gbl.var$mydata.chr,IRanges(startlist,endlist),"*",id)
data<-DataTrack(range=cprange,start,end,data=mydata.pv,name="CpG pvalue",cex=.16)
namedata_track <- AnnotationTrack(chromosome=gbl.var$mydata.chr,strand ="*",start=startlist,end=startlist,
feature="CpG",group=id,id=id, name = "feature")
return(list(data,namedata_track))
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.MYDATA\n")
}
#-------------------DRAW SINGLE MYDATA------------------
draw.plot.grid.mydata <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.GRID.MYDATA\n")
# Grab from configuration is available
if(is.null(config.var$symbol.factor)) {
tmp.cex.factor.symbol = gbl.var$cex.factor.symbol
} else {
tmp.cex.factor.symbol = config.var$symbol.factor
}
list.colors.bar <- create.color.bar(config.var, gbl.var)
color.cut <- list.colors.bar$color.cut
color.cut.ref <- list.colors.bar$color.cut.ref
#z<-color.cut[,mydata.num]
# gbl.var$fill.list[gbl.var$cur.sample]
format <- as.character(gbl.var$split.format[[1]][gbl.var$cur.sample])
if(config.var$disp.mydata) {
if(config.var$disp.type == "symbol") {
if(gbl.var$cur.sample == 1) {
#------------- DATA of INTERET
for (i in 1:nrow(gbl.var$mydata.data)) {
name.test <-gbl.var$mydata.data$MYDATA.NAME[i]
position <- gbl.var$mydata.hash.names.pos[[name.test]]
#cat ("color",i, " ", color.cut.ref[i],"\n")
if ((gbl.var$mydata.data$MYDATA.PVAL[i] > config.var$disp.pval.threshold) &
(gbl.var$mydata.data$MYDATA.PVAL[i] != 0) &
(position > (gbl.var$min.x - 1)) &
(position < (gbl.var$max.x + 1)) ) {
#---- ASSOCIATION COLOR and SIZE
mycolor <- color.cut.ref[i]
myasso <- 0
if(! is.null(config.var$disp.association)){
if(as.logical(gbl.var$split.association[[1]][gbl.var$cur.sample]) & (grepl("asso", format)[1])) {
if (config.var$verbose) cat("Association ", gbl.var$mydata.data$MYDATA.ASSO[i]," \n")
mycolor <- gbl.var$fill.list[gbl.var$cur.sample]
myasso <- gbl.var$mydata.data$MYDATA.ASSO[i]
if(grepl("-", myasso)[1]) {
if(config.var$verbose) cat("Opposited color \n")
mycolor.tmp <- opposite(mycolor,plot=FALSE)[2]
mycolor <- mycolor.tmp
} else if (gbl.var$mydata.data$MYDATA.ASSO[i] == "0") {
mycolor.tmp <- "black"
mycolor <- mycolor.tmp
}
}
}
mycex <- tmp.cex.factor.symbol
if(! is.null(config.var$disp.beta.association)){
myassoorig <- gbl.var$mydata.data$MYDATA.ASSO.ORIGINAL[i]
if(is.integer(myassoorig)){
myasso.zscore <- (myassoorig - gbl.var$mean.beta)/gbl.var$sd.beta
myasso.zscore.abs <- abs(myasso.zscore)
mycex <- tmp.cex.factor.symbol + gbl.var$myfactor.beta*myasso.zscore.abs
}
}
# if (config.var$verbose) cat("config.var$mydata.ref",config.var$mydata.ref,"\n")
# if (config.var$verbose) cat("gbl.var$mydata.data$MYDATA.NAME[i]",gbl.var$mydata.data$MYDATA.NAME[i],"\n")
# if (config.var$verbose) cat("My data",i,"vs my ref", gbl.var$mydata.best.position,"\n")
ref.print <- "FALSE"
if (exists("config.var$mydata.ref") & !is.null(config.var$mydata.ref) ) {
if (length(config.var$mydata.ref) > 0 & (gbl.var$mydata.data$MYDATA.NAME[i] == config.var$mydata.ref)){
ref.print <- "TRUE"
}
} else if ( (length(config.var$mydata.ref) > 0 ) & (i == gbl.var$mydata.best.position)){
ref.print <- "TRUE"
}
if (i == gbl.var$mydata.best.position){
ref.print <- "TRUE"
}
if (as.logical(ref.print)) {
grid.points(position,
gbl.var$mydata.data$MYDATA.PVAL[i],
pch = gbl.var$symbol.list[gbl.var$cur.sample],
gp = gpar(col = mycolor,
cex = tmp.cex.factor.symbol,
fill = "black" ,
lwd = gbl.var$line.width))
if(!is.null(config.var$disp.region)){
if(as.logical(gbl.var$split.region[[1]][gbl.var$cur.sample]) & (grepl("region", format)[1])){
# if (config.var$verbose) cat("format",format,"\n")
position.start <- gbl.var$mydata.hash.names.start[[name.test ]]
position.end <- gbl.var$mydata.hash.names.end[[name.test ]]
if(position.start < (gbl.var$min.x - 1)){
position.start <- (gbl.var$min.x - 1)
}
if(position.end > (gbl.var$max.x + 1)){
position.end <- (gbl.var$max.x + 1)
}
grid.lines(x = c(position.start,position.end),
y = c(gbl.var$mydata.data$MYDATA.PVAL[i],gbl.var$mydata.data$MYDATA.PVAL[i]),
default.units = "native", gp = gpar(lty = "solid", lwd = gbl.var$line.width, col=mycolor))
}
}
}else {
grid.points(position,
gbl.var$mydata.data$MYDATA.PVAL[i],
pch = gbl.var$symbol.list[gbl.var$cur.sample],
gp = gpar(col = "black",
cex = tmp.cex.factor.symbol,
fill = mycolor ,
lwd = gbl.var$line.width))
if(!is.null(config.var$disp.region)){
if(as.logical(gbl.var$split.region[[1]][gbl.var$cur.sample]) & (grepl("region", format)[1] )){
position.start <- gbl.var$mydata.hash.names.start[[name.test ]]
position.end <- gbl.var$mydata.hash.names.end[[name.test ]]
if(position.start < (gbl.var$min.x - 1)){
position.start <- (gbl.var$min.x - 1)
}
if(position.end > (gbl.var$max.x + 1)){
position.end <- (gbl.var$max.x + 1)
}
grid.lines(x = c(position.start,position.end),
y = c(gbl.var$mydata.data$MYDATA.PVAL[i],gbl.var$mydata.data$MYDATA.PVAL[i]),
default.units = "native", gp = gpar(lty = "solid", lwd = gbl.var$line.width, col=mycolor))
}
}
}
}
}
} else {
for (i in 1:nrow(gbl.var$mydata.data)) {
name.test <-gbl.var$mydata.data$MYDATA.NAME[i]
position <- gbl.var$mydata.hash.names.pos[[name.test ]]
if ((gbl.var$mydata.data$MYDATA.PVAL[i] > config.var$disp.pval.threshold) &
(gbl.var$mydata.data$MYDATA.PVAL[i] != 0) &
(position > (gbl.var$min.x - 1)) &
(position < (gbl.var$max.x + 1)) ) {
#---- ASSOCIATION COLOR and size
mycolor <- color.cut.ref[i]
myasso <- 0
if(! is.null(config.var$disp.association)){
if( as.logical(gbl.var$split.association[[1]][gbl.var$cur.sample]) & (grepl("asso", format)[1])) {
mycolor <- gbl.var$fill.list[gbl.var$cur.sample]
myasso <- gbl.var$mydata.data$MYDATA.ASSO[i]
if (grepl("-", myasso)[1]) {
mycolor.tmp <- opposite(mycolor,plot=FALSE)[2]
mycolor <- mycolor.tmp
} else if (gbl.var$mydata.data$MYDATA.ASSO[i] == "0") {
mycolor.tmp <- "black"
mycolor <- mycolor.tmp
}
}
}
mycex <- tmp.cex.factor.symbol
if(! is.null(config.var$disp.beta.association)){
myassoorig <- gbl.var$mydata.data$MYDATA.ASSO.ORIGINAL[i]
if(is.integer(myassoorig)){
myasso.zscore <- (myassoorig - gbl.var$mean.beta)/gbl.var$sd.beta
myasso.zscore.abs <- abs(myasso.zscore)
mycex <- tmp.cex.factor.symbol + gbl.var$myfactor.beta*myasso.zscore.abs
}
}
if (is.na(gbl.var$symbol.list[gbl.var$cur.sample])) {
grid.points(position,
gbl.var$mydata.data$MYDATA.PVAL[i],
pch = 25,
gp = gpar(col = gbl.var$color.list[gbl.var$cur.sample],
cex = tmp.cex.factor.symbol,
fill = mycolor,
lwd = gbl.var$line.width))
}
else {
grid.points(position,
gbl.var$mydata.data$MYDATA.PVAL[i],
pch = gbl.var$symbol.list[gbl.var$cur.sample],
gp = gpar(col = gbl.var$color.list[gbl.var$cur.sample],
cex = tmp.cex.factor.symbol,
fill = mycolor,
lwd = gbl.var$line.width))
}
if(! is.null(config.var$disp.region)){
if(as.logical(gbl.var$split.region[[1]][gbl.var$cur.sample]) & (grepl("region", format)[1] )){
position.start <- gbl.var$mydata.hash.names.start[[name.test ]]
position.end <- gbl.var$mydata.hash.names.end[[name.test ]]
if(position.start < (gbl.var$min.x - 1)){
position.start <- (gbl.var$min.x - 1)
}
if(position.end > (gbl.var$max.x + 1)){
position.end <- (gbl.var$max.x + 1)
}
grid.lines(x = c(position.start,position.end),
y = c(gbl.var$mydata.data$MYDATA.PVAL[i],gbl.var$mydata.data$MYDATA.PVAL[i]),
default.units = "native", gp = gpar(lty = "solid", lwd = gbl.var$line.width, col=mycolor))
}
}
}
}
}
}
else {
dev.off()
stop("Invalid display type: ", config.var$disp.type, "\n")
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.GRID.MYDATA\n")
}
#-------------------DRAW LARGE MYDATA------------------
draw.plot.grid.mydata.large <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.GRID.MYDATA.large\n")
# Grab from configuration is available
if(is.null(config.var$symbol.factor)) {
tmp.cex.factor.symbol = gbl.var$cex.factor.symbol
} else {
tmp.cex.factor.symbol = config.var$symbol.factor
}
format <- as.character(gbl.var$large.split.format[[1]][gbl.var$cur.sample.large])
if(config.var$disp.mydata) {
if(config.var$disp.type == "symbol") {
#------------- DATA LARGE
if(! is.null(config.var$mydata.large.file)) {
for (i in 1:nrow(gbl.var$mydata.large.data)) {
#---- ASSOCIATION COLOR
mycolor <- gbl.var$large.fill.list[gbl.var$cur.sample.large]
myassolarge <- 0
if(!is.null(config.var$disp.association.large)){
if(as.logical(gbl.var$large.split.association[[1]][gbl.var$cur.sample.large]) & (grepl("asso", format)[1])) {
if (config.var$verbose) cat("Association ",gbl.var$mydata.large.data$MYDATA.ASSO[i]," \n")
myassolarge <- gbl.var$mydata.large.data$MYDATA.ASSO[i]
if (grepl("-", myassolarge)[1]) {
mycolor.fill.tmp <- opposite(mycolor,plot=FALSE)[2]
mycolor <- mycolor.fill.tmp
} else if (gbl.var$mydata.large.data$MYDATA.ASSO[i] == "0") {
mycolor.fill.tmp <- "black"
mycolor <- mycolor.fill.tmp
}
}
}
mycex <- tmp.cex.factor.symbol
if(! is.null(config.var$disp.beta.association.large)){
myassolargeorig <- gbl.var$mydata.large.data$MYDATA.ASSO.ORIGINAL[i]
if(is.integer(myassolargeorig)){
myassolarge.zscore <- (myassolargeorig - gbl.var$mean.beta)/gbl.var$sd.beta
myassolarge.zscore.abs <- abs(myassolarge.zscore)
cat("original cex",tmp.cex.factor.symbol,"factor",gbl.var$myfactor.beta, " absolue ",myassolarge.zscore.abs,"\n")
mycex <- tmp.cex.factor.symbol + gbl.var$myfactor.beta*myassolarge.zscore.abs
cat("cex",mycex,"ref",tmp.cex.factor.symbol,"\n")
}
}
name.test <-gbl.var$mydata.large.data$MYDATA.NAME[i]
position <- gbl.var$mydata.large.hash.names.pos[[name.test]]
# if (config.var$verbose) cat("position",position)
if ((gbl.var$mydata.large.data$MYDATA.PVAL[i] > config.var$disp.pval.threshold) &
(gbl.var$mydata.large.data$MYDATA.PVAL[i] != 0) &
(position > (gbl.var$min.x - 1)) &
(position < (gbl.var$max.x + 1)) &
(gbl.var$mydata.large.data$MYDATA.PVAL[i] > (gbl.var$min.y - 1)) &
(gbl.var$mydata.large.data$MYDATA.PVAL[i] < (gbl.var$max.y + 1)) ) {
# if (config.var$verbose) cat("config.var$mydata.ref",config.var$mydata.ref,"\n")
# if (config.var$verbose) cat("gbl.var$mydata.data$MYDATA.NAME[i]",gbl.var$mydata.data$MYDATA.NAME[i],"\n")
if (is.na(gbl.var$large.symbol.list[gbl.var$cur.sample.large])) {
grid.points(position,
gbl.var$mydata.large.data$MYDATA.PVAL[i],
pch = 21,
gp = gpar(col = gbl.var$large.color.list[gbl.var$cur.sample.large],
cex = tmp.cex.factor.symbol,
fill = mycolor,
lwd = gbl.var$line.width))
} else {
grid.points(position,
gbl.var$mydata.large.data$MYDATA.PVAL[i],
pch = gbl.var$large.symbol.list[gbl.var$cur.sample.large],
gp = gpar(col = gbl.var$large.color.list[gbl.var$cur.sample.large],
cex = tmp.cex.factor.symbol,
fill = mycolor,
lwd = gbl.var$line.width))
}
# if (config.var$verbose) cat("format ",format,"\n")
# if (config.var$verbose) cat("Sample",gbl.var$cur.sample.large,"\n")
# if(grepl("region", format)[1] ){
# if (config.var$verbose) cat("format ",format,"\n")
# }
if (grepl("region", format)[1]){
if(! is.null(config.var$disp.region.large)) {
region.print <- "FALSE"
if(! is.null(config.var$disp.region.large)){
# if(exists("gbl.var$large.split.region[[1]][gbl.var$cur.sample.large])"){
#if(!is.null(gbl.var$large.split.region[[1]][gbl.var$cur.sample.large])){
if(as.logical(gbl.var$large.split.region[[1]][gbl.var$cur.sample.large])){
region.print <- "TRUE"
}
if(as.logical(region.print) ){
if (config.var$verbose) cat("region",gbl.var$large.split.region[[1]][gbl.var$cur.sample.large],"\n")
position.start <- gbl.var$mydata.large.hash.names.start[[name.test]]
position.end <- gbl.var$mydata.large.hash.names.end[[name.test]]
if(position.start < (gbl.var$min.x - 1)){
position.start <- (gbl.var$min.x - 1)
}
if(position.end > (gbl.var$max.x + 1)){
position.end <- (gbl.var$max.x + 1)
}
if (config.var$verbose) cat("position.start ",position.start,"\n")
if (config.var$verbose) cat("position.end ",position.end,"\n")
if (config.var$verbose) cat("y",gbl.var$mydata.large.data$MYDATA.PVAL[i],"\n")
if (config.var$verbose) cat("axis.x ", gbl.var$axis.x,"\n")
grid.lines(x = c(position.start,position.end),
y = c(gbl.var$mydata.large.data$MYDATA.PVAL[i],gbl.var$mydata.large.data$MYDATA.PVAL[i]),
default.units = "native", gp = gpar(lty = "solid", lwd = gbl.var$line.width, col=mycolor))
}
}
}
}
}
}
}
}
else {
dev.off()
stop("Invalid display type: ", config.var$disp.type, "\n")
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.GRID.MYDATA.large\n")
}
#-------------------DRAW CORMATRIX plot------------------
draw.plot.cormatrix.plot <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.CORMATRIX.PLOT\n")
cormatrix.matrix <- gbl.var$cormatrix.data
matrix.rows <- dim(cormatrix.matrix)[1]
matrix.cols <- dim(cormatrix.matrix)[2]
list.colors.bar <- create.color.bar(config.var, gbl.var)
color.cut <- list.colors.bar$color.cut
cormatrix.key <- list.colors.bar$cormatrix.key
map.label.ldtype <- list.colors.bar$map.label.ldtype
map.label.distance <- list.colors.bar$map.label.distance
#cat ("color",1, " ", color.cut)
x.x <- (1:matrix.cols)/matrix.cols
y.y <- (1:matrix.rows)/matrix.rows
right <- rep(x.x, nrow(gbl.var$general.data))
top <- rep(y.y, each=matrix.cols)
image.rect <- rectGrob(x=right,
y=top,
width=1/matrix.cols,
height=1/matrix.rows,
just=c("right", "top"),
gp=gpar(col=NULL,
fill=color.cut,
lty="blank"),
name="image.rect")
#seq.x <- c(1*(1/gbl.var$mydata.num), 1)
#seq.y <- c(0, (1 - (1/gbl.var$mydata.num)))
tmp.mydata.num <- gbl.var$mydata.num
seq.x.names <- seq((1/tmp.mydata.num), 1, by=(1/tmp.mydata.num))
seq.y.names <- seq(0, (1 - (1/tmp.mydata.num)), by=(1/tmp.mydata.num))
#The condition for the tmp.mydata.num is met in the original construction of the sequence
if(tmp.mydata.num > 50) {
tmp.x.factor <- seq.x.names[1]
seq.x.names <- seq.x.names + tmp.x.factor/2
seq.y.names <- seq.y.names - tmp.x.factor/2
} else if(tmp.mydata.num < 50) {
tmp.x.factor <- (seq.x.names[1] - 0.02)/2 + 0.02
tmp.y.factor <- (seq.x.names[1] - 0.02)/2
seq.x.names <- seq(tmp.x.factor, (1 - tmp.y.factor), by=(1/tmp.mydata.num))
seq.y.names <- seq(tmp.y.factor, (1 - tmp.y.factor), by=(1/tmp.mydata.num))
}
mydata.names.pos.x <- (1:gbl.var$mydata.num)/gbl.var$mydata.num
mydata.names.pos.y <- ((1:gbl.var$mydata.num)/gbl.var$mydata.num - 1/gbl.var$mydata.num)
###Factor for the size of name
# if(is.null(config.var$font.factor)) {
# tmp.font.factor = (gbl.var$cex.factor - 0.5)
# } else {
# tmp.font.factor = as.numeric(config.var$font.factor)
#}
tmp.font.factor = (gbl.var$cex.factor - 0.5)
if (config.var$disp.mydata.names) {
if( length(gbl.var$sorted.mydata.names) < 30) {
list.name <- paste(" ",gbl.var$sorted.mydata.names)
name.ref <- paste(" ",gbl.var$sorted.mydata.names[gbl.var$mydata.ref.pos])
} else {
list.name <- paste("",gbl.var$sorted.mydata.names)
name.ref <- paste("",gbl.var$sorted.mydata.names[gbl.var$mydata.ref.pos])
}
rot.name <- -45
#if (config.var$cormatrix.format == "raw") {
# rot.name <- 135
#}
mydata.names.cormatrix.sec <- textGrob(rev(list.name),
x = seq.x.names[1:gbl.var$mydata.num],
y = seq.y.names[1:gbl.var$mydata.num],
rot=rot.name,
gp=gpar(cex = tmp.font.factor),
just = c("left"),
name="mydata.names.cormatrix.sec")
if(config.var$disp.color.ref) {
#REFERENCE
mydata.names.cormatrix.sec.ref <- textGrob(rev(name.ref),
x = seq.x.names[gbl.var$mydata.ref.pos],
y = seq.y.names[gbl.var$mydata.ref.pos],
rot=rot.name,
gp=gpar(cex = tmp.font.factor,col="darkorchid1"),
just = c("left"),
name="mydata.names.cormatrix.sec")
}
}
popViewport()
#67.5
##### VIEW PORT FOR LD MAP
cormatrix.map.vp <- viewport(y = unit(0.415, "npc"),
x = unit(0.471875, "npc"),
width = unit(0.7, "snpc"),
height = unit(0.7, "snpc"),
angle = 67.5,
just = c("center", "center"),
name = "cormatrix.map.vp")
if (config.var$disp.mydata.names) {
if(config.var$disp.color.ref) {
cormatrix.map <- gTree(children=gList(image.rect, mydata.names.cormatrix.sec, mydata.names.cormatrix.sec.ref), just=c("center", "bottom"), vp=cormatrix.map.vp, name="cormatrix.map")
} else {
cormatrix.map <- gTree(children=gList(image.rect, mydata.names.cormatrix.sec), just=c("center", "bottom"), vp=cormatrix.map.vp, name="cormatrix.map")
}
} else {
cormatrix.map <- gTree(children=gList(image.rect), just=c("center"), vp=cormatrix.map.vp, name="cormatrix.map")
}
gene.map.vp <- viewport(name = "gene.map.vp")
gene.map <- gTree(children=gList(map.label.ldtype, map.label.distance), vp = gene.map.vp, name="gene.map")
pushViewport(cormatrix.map.vp)
grid.draw(cormatrix.map)
popViewport()
pushViewport(gene.map.vp)
grid.draw(gene.map)
if(config.var$disp.color.bar) {
#DEBUG STATEMENT
# if (config.var$verbose) cat("is.null(cormatrix.key) ", is.null(cormatrix.key), "\n")
grid.draw(cormatrix.key)
}
popViewport()
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.CORMATRIX.PLOT\n")
}
#-------------------DRAW LEGEND----------------------------
draw.legend <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.LEGEND\n")
#DEBUG STATEMENT
# if (config.var$verbose) cat("gbl.var$font.size ", gbl.var$font.size, "\n")
if(config.var$disp.cormatrixmap) {
legend.vp <- viewport(x = 0.5, y = -2, height = 1, width = 1, name = "legend.vp")
}
else {
legend.vp<- viewport(x = 0.5, y = 0.05, height = 1, width = 1, name = "legend.vp")
}
pushViewport(legend.vp)
#-------------------LEGEND SAMPLES BEGINS-----------------------
legend.samples.list <- NULL
legend.samples <- gTree(children=NULL,
just=c("center", "bottom"), vp=legend.vp,
name="legend.samples")
samples <- gbl.var$samples
if(samples <= 8) {
y.pos.sec.row.correction <- 0
x.pos.sec.row.correction <- 0
#--------------- LEGEND FOR REFERENCE
# if (config.var$verbose) cat("Reference \n")
#Ensure that labels do not overlap by moving them
if(config.var$disp.cormatrixmap) {
y.pos <- .8
x.pos <- 0.75
} else {
y.pos <- -0.3125 + y.pos.sec.row.correction
x.pos <- -0.19 + x.pos.sec.row.correction
}
label.text.ref <- gbl.var$mydata.data$MYDATA.NAME[which(gbl.var$mydata.data$LOC == gbl.var$mydata.ref.pos)]
label.sample.text <- textGrob(label.text.ref,
x = (x.pos + 0.035),
y = y.pos,
just=("left"),
gp = gpar(fontsize = gbl.var$font.size *0.75 * config.var$font.factor))
#FOR LD adjust is .3
#FOR NO-LD adjust is
label.sample.symbol <- pointsGrob(x = x.pos,
y = y.pos,
pch = 21,
gp = gpar(col = "darkorchid1",
cex = (gbl.var$cex.factor - 0.5),
lwd = gbl.var$line.width,
fill = "black"))
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.text
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.symbol
#All samples
# if (config.var$verbose) cat("All samples \n")
for(i in 1:samples) {
if(i > 3) {
x.pos.sec.row.correction <- -1.5
y.pos.sec.row.correction <- -.04
}
#label.text <- substr(gbl.var$split.sample.labels[[1]][i],1, 30)
label.text <- gbl.var$split.sample.labels[[1]][i]
#Ensure that labels do not overlap by moving them
if(config.var$disp.cormatrixmap) {
y.pos <- .8 + 0.1 * i
x.pos <- 0.75
} else {
y.pos <- -0.3125 + y.pos.sec.row.correction
x.pos <- -0.19 + 0.35* i + x.pos.sec.row.correction
}
label.sample.text <- textGrob(label.text,
x = (x.pos + 0.035),
y = y.pos,
just=("left"),
gp = gpar(fontsize = (gbl.var$font.size)*0.75 * (config.var$font.factor)))
if(is.na(gbl.var$symbol.list[i])) {
gbl.var$symbol.list[i] <- "circle-fill"
}
#FOR LD adjust is .3
#FOR NO-LD adjust is
label.sample.symbol <- pointsGrob(x = x.pos,
y = y.pos,
pch = gbl.var$symbol.list[i],
gp = gpar(col = "black",
cex = (gbl.var$cex.factor - 0.5),
lwd = gbl.var$line.width,
fill = gbl.var$fill.list[i]))
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.text
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.symbol
}
#--------------- LEGEND LARGE DATA
if(! is.null(config.var$mydata.large.file)){
large.samples <- gbl.var$large.samples
for(i in 1:large.samples) {
if((samples + i) > 3) {
x.pos.sec.row.correction <- -1.5
y.pos.sec.row.correction <- -.04
}
#label.text <- substr(gbl.var$large.split.sample.labels[[1]][i], 1, 30)
label.text <- gbl.var$large.split.sample.labels[[1]][i]
#Ensure that labels do not overlap by moving them
if(config.var$disp.cormatrixmap) {
y.pos <- .8 + 0.1 * (samples + i )
x.pos <- 0.75
} else {
y.pos <- -0.3125 + y.pos.sec.row.correction
x.pos <- -0.19 + 0.35* ( samples + i ) + x.pos.sec.row.correction
}
label.sample.text <- textGrob(label.text,
x = (x.pos + 0.035),
y = y.pos,
just=("left"),
gp = gpar(fontsize = (gbl.var$font.size) *0.75 * config.var$font.factor))
if(is.na(gbl.var$large.symbol.list[i])) {
gbl.var$large.symbol.list[i] <- 24
}
#FOR LD adjust is .3
#FOR NO-LD adjust is
label.sample.symbol <- pointsGrob(x = x.pos,
y = y.pos,
pch = gbl.var$large.symbol.list[i],
gp = gpar(col = gbl.var$large.color.list[i],
cex = (gbl.var$cex.factor - 0.5),
lwd = gbl.var$line.width,
fill = gbl.var$large.fill.list[i]))
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.text
legend.samples.list[[(length(legend.samples.list) + 1)]] <- label.sample.symbol
}
}
class(legend.samples.list) <- c("gList")
legend.glist.samples <- legend.samples.list
legend.samples <- gTree(children=legend.glist.samples,
just=c("left", "bottom"),
vp=legend.vp,
name="legend.samples")
grid.draw(legend.samples)
}
popViewport()
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.LEGEND\n")
}
#-------------------DRAW MYDATA NAME----------------------------
#draw MYDATA labels
draw.plot.grid.mydata.names <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.PLOT.GRID.MYDATA.NAMES\n")
tmp.correction.factor <- gbl.var$equidis.pos[1] * 10^(gbl.var$cur.exp - 9) * (1 + config.var$connecting.lines.adj)
#DEBUG STATEMENT
# if (config.var$verbose) cat("config.var$disp.cormatrixmap ", config.var$disp.cormatrixmap, "\n")
if (config.var$verbose) cat("length(gbl.var$sorted.mydata.names) ", length(gbl.var$sorted.mydata.names), "\n")
# if (config.var$verbose) cat("tmp.correction.factor ", tmp.correction.factor, "\n")
# if (config.var$verbose) cat("gbl.var$axis.y[1] ", gbl.var$axis.y[1], "\n")
if(!config.var$disp.cormatrixmap) {
if( length(gbl.var$sorted.mydata.names) < 30) {
list.name <- paste(" ",gbl.var$sorted.mydata.names)
name.ref <- paste(" ",gbl.var$sorted.mydata.names[gbl.var$mydata.ref.pos])
} else {
list.name <- paste("",gbl.var$sorted.mydata.names)
name.ref <- paste("",gbl.var$sorted.mydata.names[gbl.var$mydata.ref.pos])
}
rot.name <- 90
if (config.var$cormatrix.format == "raw") {
rot.name <- -90
}
if(config.var$image.size == 3.5) {
if( length(list.name) < 30) {
mydata.names.grob <- textGrob(list.name, x = gbl.var$equidis.pos, y = unit(-8, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 1))), just=c("left"), name="mydata.names")
if(config.var$disp.color.ref) {
#Ref
mydata.names.grob.ref <- textGrob(name.ref, x = gbl.var$equidis.pos[gbl.var$mydata.ref.pos], y = unit(-8, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 1) ),col="darkorchid1"), just=c("left"), name="mydata.names.ref")
}
} else {
mydata.names.grob <- textGrob(list.name, x = gbl.var$equidis.pos, y = unit(-15, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 1) )), just=c("left"), name="mydata.names")
if(config.var$disp.color.ref) {
#Ref
mydata.names.grob.ref <- textGrob(name.ref, x = gbl.var$equidis.pos[gbl.var$mydata.ref.pos], y = unit(-15, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 1)),col="darkorchid1"), just=c("left"), name="mydata.names.ref")
}
}
} else if (config.var$image.size == 7) {
if( length(gbl.var$sorted.mydata.names) < 30) {
mydata.names.grob <- textGrob(list.name, x = gbl.var$equidis.pos, y = unit(-8, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 2) )), just=c("left"), name="mydata.names")
if(config.var$disp.color.ref) {
#Ref
mydata.names.grob.ref <- textGrob(name.ref, x = gbl.var$equidis.pos[gbl.var$mydata.ref.pos], y = unit(-8, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize =((gbl.var$font.size - 2)),col="darkorchid1"), just=c("left"), name="mydata.names.ref")
}
}else {
mydata.names.grob <- textGrob(list.name, x = gbl.var$equidis.pos, y = unit(-15, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize = ((gbl.var$font.size - 2))), just=c("left"), name="mydata.names")
if(config.var$disp.color.ref) {
#Ref
mydata.names.grob.ref <- textGrob(name.ref, x = gbl.var$equidis.pos[gbl.var$mydata.ref.pos], y = unit(-15, "char"),
rot=rot.name, default.units = "native",
gp=gpar(fontsize =((gbl.var$font.size - 2)),col="darkorchid1"), just=c("left"), name="mydata.names.ref")
}
}
}
if(config.var$disp.mydata.names) {
grid.draw(mydata.names.grob)
if(config.var$disp.color.ref) {
grid.draw(mydata.names.grob.ref)
}
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.PLOT.GRID.MYDATA.NAMES\n")
}
#------------------------------------------------------
#------------- SET PARAMETER DRAW (color, symbole)-----
#------------- CREATE COLOR BAR ------------------------
create.color.bar <- function(config.var, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE COLOR BAR\n")
cormatrix.matrix.ref <- gbl.var$ref
cormatrix.matrix <- gbl.var$cormatrix.data
cormatrix.pvalue.matrix <- gbl.var$cormatrix.pvalue.data.full
if(config.var$use.colors) {
if(config.var$cormatrix.color.scheme == "heat") {
cormatrix.colors <- heat.colors(gbl.var$palette.size)
} else if(config.var$cormatrix.color.scheme == "cm") {
cormatrix.colors <- cm.colors(gbl.var$palette.size)
} else if(config.var$cormatrix.color.scheme == "custom") {
if(!is.null(config.var$palette.file)) {
tmp.colors <- read.table(config.var$palette.file, as.is=TRUE, header=FALSE, blank.lines.skip = TRUE, fill=TRUE)
gbl.var$palette.size <- length(tmp.colors$V1)
custom.colors <- paste("#", tmp.colors$V1, sep="")
cormatrix.colors <- rev(custom.colors)
}
else {
dev.off()
stop("palette.file must be specified\n")
}
}
else if(config.var$cormatrix.color.scheme == "topo") {
cormatrix.colors <- topo.colors(gbl.var$palette.size)
}
else if(config.var$cormatrix.color.scheme == "gray") {
cormatrix.colors <- gray.colors(gbl.var$palette.size)
} else if(config.var$cormatrix.color.scheme == "bluetored"){
cormatrix.colors <- colorRampPalette(c("blue","red"))(gbl.var$palette.size)
} else if(config.var$cormatrix.color.scheme == "bluewhitered"){
cormatrix.colors <- colorRampPalette(c("blue","white","red"))(gbl.var$palette.size)
}
else {
dev.off()
stop("Invalid color scheme: ", config.var$cormatrix.color.scheme, "\n")
}
}
else {
cormatrix.colors <- gray.colors(gbl.var$palette.size)
}
#color.bar.colors <- c(rep(NA, gbl.var$palette.size), cormatrix.colors[gbl.var$palette.size:1])
color.bar.colors <- c(rep(NA, gbl.var$palette.size), cormatrix.colors[gbl.var$palette.size:1])
#DEBUG STATEMENT
# if (config.var$verbose) cat("color.bar.colors ", color.bar.colors, "\n")
#height=0.125
color.bar <- rectGrob(x=rep(seq(1:gbl.var$palette.size)/gbl.var$palette.size, 2),
y=rep(seq(1:2)/2, each=gbl.var$palette.size),
width=(1/gbl.var$palette.size),
height=0.075,
just=c("right", "top"),
gp=gpar(col=NULL,
fill=color.bar.colors,
cex = (gbl.var$cex.factor + 0.2),
lty="blank"),
name = "color.bar")
# color.bar.labels <- textGrob(paste(c(-1,-0.6,-0.2,0.2,0.6,1)), x=0.2*0:5, y=0.8, gp=gpar(fontsize = gbl.var$font.size), name="color.bar.labels")
color.bar.labels <- textGrob(paste(c(1,0.6,0.2,-0.2,-0.6,-1)), x=0.2*0:5, y=0.8, gp=gpar(fontsize = (gbl.var$font.size *config.var$font.factor)), name="color.bar.labels")
cormatrix.key.vp <- viewport(x=0.2, y=-0.03, width = 0.25, height = 0.25)
cormatrix.key <- gTree(children=gList(color.bar, color.bar.labels), name = "cormatrix.key", vp=cormatrix.key.vp)
if(config.var$disp.phys.dist) {
if(gbl.var$total.dist > 1000) {
map.label.text.distance <- paste("Physical Distance: ", round(gbl.var$total.dist/1000, 1), " kb", sep="")
} else {
map.label.text.distance <- paste("Physical Distance: ", gbl.var$total.dist, " bases", sep="")
}
} else {
map.label.text.distance <- " "
}
if (config.var$cormatrix.method == "spearman") {
map.label.text.ldtype <- "Correlation Matrix Map Type: Spearman"
} else if (config.var$cormatrix.method == "pearson") {
map.label.text.ldtype <- "Correlation Matrix Map Type: Pearson"
} else if (config.var$cormatrix.method == "kendall") {
map.label.text.ldtype <- "Correlation Matrix Map Type: Kendall"
} else {
dev.off()
stop("Invalid CORMATRIX metric : ", config.var$cormatrix.method, "\n")
}
map.label.distance <- textGrob(map.label.text.distance,
x = 0.2,
y = 0.1425,
just=("center"),
gp = gpar(fontsize = (gbl.var$font.size * config.var$font.factor)),
name="map.label.distance")
map.label.ldtype <- textGrob(map.label.text.ldtype,
x = 0.2,
y = 0.11150,
just=("center"),
gp = gpar(fontsize = (gbl.var$font.size *config.var$font.factor)),
name="map.label.ldtype")
matrix.rows <- dim(cormatrix.matrix)[1]
matrix.cols <- dim(cormatrix.matrix)[2]
intervals<-2/(length(cormatrix.colors))
color.intervals <- seq(-1,1,by=intervals)
# cat(length(color.intervals),"\n")
# cat(length(cormatrix.colors),"\n")
#Create the color of correlation matrix
tmp.color.cut <- as.character(cut(cormatrix.matrix, color.intervals, labels=as.character(cormatrix.colors)))
color.cut.ref <- as.character(cut(cormatrix.matrix.ref, color.intervals, labels=as.character(cormatrix.colors)))
tmp.vector <- NULL
for(i in seq(0, matrix.rows - 1)) {
for(j in seq(matrix.rows, 1, by =-1)) {
tmp.vector <- c(tmp.vector, (matrix.rows*j-i))
}
}
#List of case to put white
blank.vector <- NULL
for(i in seq(0, matrix.rows -1)) {
for(j in seq(1, (matrix.rows-i + 1), by =1)) {
blank.vector <- c(blank.vector, (matrix.rows*j-i))
}
}
color.cut <- rep(NULL, matrix.rows^2)
for(i in 1:matrix.rows^2) {
if(config.var$cormatrix.format == "raw" |
config.var$cormatrix.format == "raw_rev" |
config.var$cormatrix.format == "DTR_RAW") {
#Define row and colunm number from i
r <- (as.integer(i/matrix.rows))
r.tmp <- i/matrix.rows
if(r.tmp%%1==0){
# if (config.var$verbose) cat("integer")
} else {
r <- r + 1
}
c <- i - (r-1)*matrix.rows
v<- cormatrix.pvalue.matrix[r,c]
if (config.var$verbose) cat ("Pvalue in ",i,":",r,"-",c," is ",v,"\n")
if( cormatrix.pvalue.matrix[r,c] <= config.var$cormatrix.sig.level) {
color.cut[i] <- tmp.color.cut[tmp.vector[i]]
} else if(tmp.vector[i] %in% blank.vector){
#it is blank value
color.cut[i] <- tmp.color.cut[tmp.vector[i]]
} else {
color.cut[i] <- "ghostwhite"
}
} else {
color.cut[i] <- tmp.color.cut[tmp.vector[i]]
}
}
if (config.var$verbose) cat("FINISH CREATE.COLOR.BAR\n")
return(list(color.cut = color.cut, color.cut.ref =color.cut.ref, cormatrix.key = cormatrix.key, map.label.ldtype = map.label.ldtype, map.label.distance = map.label.distance))
}
#-------------------CREATE LIST of COLOR----------------------------
create.color.list <- function(config.var,gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.color.list\n")
if(config.var$use.colors) {
tmp.color.list <- c("red", "blue", "green", "black", "orange")
}
else {
tmp.color.list <- c("grey0", "grey20", "grey40", "grey60", "grey80")
}
if(!is.null(config.var$color.list)) {
split.tmp.color.list <- strsplit(config.var$color.list, ",")
if(gbl.var$mydata.samples != length(split.tmp.color.list[[1]])) {
dev.off()
stop("The color list must have ", gbl.var$mydata.samples, " colors separated by commas without spaces.\n")
}
} else {
if(gbl.var$mydata.samples <= 5) {
split.tmp.color.list <- list(head(tmp.color.list, gbl.var$mydata.samples))
} else {
dev.off()
stop("coMET includes a default set of colors for 5 samples. For more samples, please specify color.list\n")
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.color.list\n")
return(split.tmp.color.list)
}
#-------------------CREATE LIST of COLOR FOR LARGE DATA----------------------------
create.color.list.large <- function(config.var,gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.color.list.large\n")
if(config.var$use.colors) {
tmp.color.list <- c("red", "blue", "green", "black", "orange")
}
else {
tmp.color.list <- c("grey0", "grey20", "grey40", "grey60", "grey80")
}
if(!is.null(config.var$color.list.large)) {
large.split.tmp.color.list <- strsplit(config.var$color.list.large, ",")
if(gbl.var$large.mydata.samples != length(large.split.tmp.color.list[[1]])) {
dev.off()
stop("The color list must have ", gbl.var$large.mydata.samples, " colors separated by commas without spaces.\n")
}
} else {
if(gbl.var$large.mydata.samples <= 5) {
large.split.tmp.color.list <- list(head(tmp.color.list, gbl.var$large.mydata.samples))
} else {
dev.off()
stop("coMET includes a default set of colors for 5 samples. For more samples, please specify color.list.large\n")
}
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.color.list.large\n")
return(large.split.tmp.color.list)
}
#-------------------CREATE LIST of SYMBOLE----------------------------
create.symbol.list <- function(config.var, split.color.list, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.SYMBOL.LIST\n")
tmp.symbol.list <- c("circle-fill", "square-fill", "diamond-fill", "triangle-fill", "circle")
if(!is.na(config.var$symbols)) {
split.tmp.symbol.list <- strsplit(config.var$symbols, ",")
if(gbl.var$mydata.samples != length(split.tmp.symbol.list[[1]])) {
dev.off()
stop("The symbol list must have ", gbl.var$mydata.samples, " symbol(s) separated by commas without spaces.\n")
}
} else {
if(gbl.var$mydata.samples <= 5) {
split.tmp.symbol.list <- list(head(tmp.symbol.list, gbl.var$mydata.samples))
} else {
dev.off()
stop("coMET includes a default set of colors for 5 samples. For more samples, please specify symbols\n")
}
}
split.symbol.list <- NULL
for(i in 1:gbl.var$mydata.samples) {
if(any(grep("circle", split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
split.symbol.list <- c(split.symbol.list, 21)
} else if(any(grep("square", split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
split.symbol.list <- c(split.symbol.list, 22)
} else if(any(grep("diamond", split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
split.symbol.list <- c(split.symbol.list, 23)
} else if(any(grep("triangle", split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
split.symbol.list <- c(split.symbol.list, 24)
} else if(any(grep("NA", split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
split.symbol.list <- c(split.symbol.list, NA)
} else {
dev.off()
stop("Unknown symbol: ", split.tmp.symbol.list[[1]][i], "\n")
}
}
split.fill.list <- list(rep("white", gbl.var$mydata.samples))
fill.pos <- grep("fill", split.tmp.symbol.list[[1]], ignore.case = TRUE)
#DEBUG STATEMENT
# if (config.var$verbose) cat("fill.pos ", fill.pos, "\n")
split.fill.list[[1]][fill.pos] <- split.color.list[[1]][fill.pos]
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.SYMBOL.LIST\n")
return(list(split.symbol.list = split.symbol.list, split.fill.list = split.fill.list))
}
#-------------------CREATE LIST of SYMBOLE FOR LARGE DATA----------------------------
create.symbol.list.large <- function(config.var, large.split.color.list, gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.SYMBOL.LIST.large\n")
large.tmp.symbol.list <- c("circle-fill", "square-fill", "diamond-fill", "triangle-fill", "circle")
if(!is.na(config.var$symbols.large)) {
large.split.tmp.symbol.list <- strsplit(config.var$symbols.large, ",")
if(gbl.var$large.mydata.samples != length(large.split.tmp.symbol.list[[1]])) {
dev.off()
stop("The symbol list must have ", gbl.var$large.mydata.samples, " symbol(s) separated by commas without spaces.\n")
}
} else {
if(gbl.var$large.mydata.samples <= 5) {
large.split.tmp.symbol.list <- list(head(large.tmp.symbol.list, gbl.var$large.mydata.samples))
} else {
dev.off()
stop("coMET includes a default set of colors for 5 samples. For more samples, please specify symbols\n")
}
}
large.split.symbol.list <- NULL
for(i in 1:gbl.var$large.mydata.samples) {
if(any(grep("circle", large.split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
large.split.symbol.list <- c(large.split.symbol.list, 21)
} else if(any(grep("square", large.split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
large.split.symbol.list <- c(large.split.symbol.list, 22)
} else if(any(grep("diamond", large.split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
large.split.symbol.list <- c(large.split.symbol.list, 23)
} else if(any(grep("triangle", large.split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
large.split.symbol.list <- c(large.split.symbol.list, 24)
} else if(any(grep("NA", large.split.tmp.symbol.list[[1]][i], ignore.case = TRUE))) {
large.split.symbol.list <- c(large.split.symbol.list, NA)
} else {
dev.off()
stop("Unknown symbol: ", large.split.tmp.symbol.list[[1]][i], "\n")
}
}
large.split.fill.list <- list(rep("white", gbl.var$large.mydata.samples))
large.fill.pos <- grep("fill", large.split.tmp.symbol.list[[1]], ignore.case = TRUE)
#DEBUG STATEMENT
# if (config.var$verbose) cat("large.fill.pos ", large.fill.pos, "\n")
large.split.fill.list[[1]][large.fill.pos] <- large.split.color.list[[1]][large.fill.pos]
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.SYMBOL.LIST.large\n")
return(list(large.split.symbol.list = large.split.symbol.list, large.split.fill.list = large.split.fill.list))
}
#-------------------DRAW GENES NAMES for WEB PAGE----------------------------
draw.name.genes.web <- function(config.var,gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START DRAW.NAME.GENES.WEB\n")
#DEBUG STATEMENT
# if (config.var$verbose) cat("gbl.var$font.size ", gbl.var$font.size, "\n")
popViewport()
top.vp <- gbl.var$top.vp
gene.name.vp.cormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 4,
layout.pos.col = 3,
just=c("left", "top"),
name = "gene.name.vp.cormatrixmap")
gene.name.vp.nocormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 5,
layout.pos.col = 3,
just=c("left", "top"),
name = "gene.namen.vp.nocormatrixmap")
if(config.var$disp.cormatrixmap) {
pushViewport(vpTree(top.vp, vpList(gene.name.vp.cormatrixmap)))
gene.name.vp <- gene.name.vp.cormatrixmap
}
else {
pushViewport(vpTree(top.vp, vpList(gene.name.vp.nocormatrixmap)))
gene.name.vp <- gene.name.vp.nocormatrixmap
}
#-------------------NAME of GENES BEGINS-----------------------
name.genes <- genesName_ENSEMBL(config.var$genome,gbl.var$mydata.chr,gbl.var$min.x,gbl.var$max.x,config.var$dataset.gene)
legend.name.genes.list <- NULL
if( !is.null(name.genes)) {
if(nrow(name.genes) <= 10) {
#All name.genes
# if (config.var$verbose) cat("All name.genes \n")
for(i in 1:nrow(name.genes)) {
label.text <- name.genes[i,2]
# if (config.var$verbose) cat("Gene",i,":", label.text,"\n")
#Ensure that labels do not overlap by moving them
y.pos <- 1.8 - 0.3 * ( i - 1)
x.pos <- 0.75
label.name.genes.text <- textGrob(label.text,
x = x.pos,
y = y.pos,
just=("left"),
gp = gpar(fontsize = ((gbl.var$font.size * 0.7 )),fontface = "bold"))
legend.name.genes.list[[(length(legend.name.genes.list) + 1)]] <- label.name.genes.text
}
class(legend.name.genes.list) <- c("gList")
legend.glist.name.genes <- legend.name.genes.list
# just=c("left", "top"),
legend.name.genes <- gTree(children=legend.glist.name.genes,
vp=gene.name.vp,
name="legend.gene.name")
grid.draw(legend.name.genes)
}
popViewport()
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.NAME.GENES.WEB\n")
return(gbl.var)
}
#-------------------DRAW NAMES OF TRACKS for WEB PAGE----------------------------
draw.name.tracks.web <- function(config.var,gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.NAME.TRACKS.WEB\n")
#DEBUG STATEMENT
# if (config.var$verbose) cat("gbl.var$font.size ", gbl.var$font.size, "\n")
popViewport()
top.vp <- gbl.var$top.vp
name.tracks.vp.cormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 4,
layout.pos.col = 1,
name = "name.tracks.vp.cormatrixmap")
name.tracks.vp.nocormatrixmap <- viewport(height = 1,
width = 1,
layout.pos.row = 5,
layout.pos.col = 1,
name = "name.tracks.vp.nocormatrixmap")
name.tracks.vp.cormatrixmap.nopval <- viewport(height = 1,
width = 1,
layout.pos.row = 3,
layout.pos.col = 1,
name = "name.tracks.vp.nocormatrixmap.nopval")
if(config.var$disp.cormatrixmap) {
if(config.var$disp.pvalueplot) {
pushViewport(vpTree(top.vp, vpList(name.tracks.vp.cormatrixmap)))
name.tracks.vp <- name.tracks.vp.cormatrixmap
} else {
pushViewport(vpTree(top.vp, vpList(name.tracks.vp.cormatrixmap.nopval)))
name.tracks.vp <- name.tracks.vp.cormatrixmap.nopval
}
}
else {
pushViewport(vpTree(top.vp, vpList(name.tracks.vp.nocormatrixmap)))
name.tracks.vp <- name.tracks.vp.nocormatrixmap
}
#-------------------NAME of TRACKS BEGINS-----------------------
legend.tracks.list <- NULL
y.label.pos <- c(1.25,0, -0.35,-0.85,-1.15,-1.45,-1.75)
num.tracks <- 1
if(config.var$image.size == 3.5) {
#All tracks cf order define via create.tracks.web
# if (config.var$verbose) cat("All tracks \n")
y.label.pos <- c(1.25,0.15, -0.25,-0.75,-1.25,-1.65,-1.95)
} else if(config.var$image.size == 7) {
y.label.pos <- c(1.25,0.30, -0.1, -0.7, -1.3, -1.7, -2.1)
}
#--- GENES ENSEMBL
if(has.key("geneENSEMBL", gbl.var$split.list.tracks)) {
label.tracks.text.ensembl <- textGrob("ENSEMBL Genes",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size*0.75*config.var$font.factor),
fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.ensembl
num.tracks <- num.tracks + 1
}
if(has.key("transcriptENSEMBL", gbl.var$split.list.tracks)) {
label.tracks.text.ensembl <- textGrob("ENSEMBL Transcripts",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size*0.75*config.var$font.factor),
fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.ensembl
num.tracks <- num.tracks + 1
}
#--- genes UCSC
if(has.key("genesUCSC",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("genes UCSC",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- xenogenes UCSC
if(has.key("xenogenesUCSC",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("xeno genes UCSC",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- CG Island
if(has.key("CGI",gbl.var$split.list.tracks)) {
label.tracks.text.cgisland <- textGrob("CG Island",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor ),
fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.cgisland
num.tracks <- num.tracks + 1
}
#--- ChromatinHMM
if(has.key("ChromHMM",gbl.var$split.list.tracks)) {
label.tracks.text.chromatinhmm <- textGrob("Broad ChromHMM",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),
fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.chromatinhmm
num.tracks <- num.tracks + 1
}
#--- DNAse
if(has.key("DNAse",gbl.var$split.list.tracks)) {
label.tracks.text.dnase <- textGrob("DNase Clusters",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.dnase
num.tracks <- num.tracks + 1
}
#--- Regulation ENSEMBL
if(has.key("RegENSEMBL",gbl.var$split.list.tracks)) {
label.tracks.text.reg <- textGrob("Regulation ENSEMBL",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.reg
num.tracks <- num.tracks + 1
}
#--- SNP
if(has.key("SNP",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("SNP UCSC",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- SNPstoma
if(has.key("SNPstoma",gbl.var$split.list.tracks)) {
label.tracks.text.chromatinhmm <- textGrob("SNP stomatic cells",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.chromatinhmm
num.tracks <- num.tracks + 1
}
#--- SNPstru
if(has.key("SNPstru",gbl.var$split.list.tracks)) {
label.tracks.text.dnase <- textGrob("structural SNP",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.dnase
num.tracks <- num.tracks + 1
}
#--- SNPstrustoma
if(has.key("SNPstrustoma",gbl.var$split.list.tracks)) {
label.tracks.text.dnase <- textGrob(" stomatic stuctural SNP",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.dnase
num.tracks <- num.tracks + 1
}
#--- ISCA
if(has.key("ISCA",gbl.var$split.list.tracks)) {
label.tracks.text.reg <- textGrob("ISCA",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.reg
num.tracks <- num.tracks + 1
}
#--- COSMIC
if(has.key("COSMIC",gbl.var$split.list.tracks)) {
label.tracks.text.reg <- textGrob("COSMIC",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.reg
num.tracks <- num.tracks + 1
}
#--- GAD
if(has.key("GAD",gbl.var$split.list.tracks)) {
label.tracks.text.reg <- textGrob("GAD",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.reg
num.tracks <- num.tracks + 1
}
#--- ClinVar
if(has.key("ClinVar",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("ClinVar",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- GeneReviews
if(has.key("GeneReviews",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("GeneReviews",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- GWAS
if(has.key("GWAS",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("GWAS",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- ClinVarCNV
if(has.key("ClinVarCNV",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("ClinVarCNV",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- GC content
if(has.key("GCcontent",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("GC content",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75 *config.var$font.factor),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
#--- Repeat Element
if(has.key("RepeatElt",gbl.var$split.list.tracks) ){
label.tracks.text.snp <- textGrob("Repeat elements",
x = -0.25,
y = y.label.pos[num.tracks],
just=c("right"),
gp = gpar(fontsize = (gbl.var$font.size *0.75*config.var$font.factor ),fontface = "bold"))
legend.tracks.list[[num.tracks]] <- label.tracks.text.snp
num.tracks <- num.tracks + 1
}
class(legend.tracks.list) <- c("gList")
legend.glist.tracks <- legend.tracks.list
# just=c("left", "top"),
legend.tracks <- gTree(children=legend.glist.tracks,
vp=name.tracks.vp,
name="legend.tracks")
grid.draw(legend.tracks)
popViewport()
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH DRAW.NAME.TRACKS.WEB\n")
return(gbl.var)
}
#------------------ CREATE TRACKS for USER ------------------------------
create.tracks.user <- function(config.var,gbl.var){
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.TRACKS.USER\n")
if(!is.null(config.var$biofeat.user.file)){
split.biofeature.data.user.file <- gbl.var$split.biofeature.data.user.file
split.biofeature.data.user.type <- gbl.var$split.biofeature.data.user.type
split.biofeature.data.user.type.plot <- gbl.var$split.biofeature.data.user.type.plot
num.data=0
listtracks_user <- list()
track.biofeat <- NULL
cur.biofeat <- 0
for(i in 1:length(split.biofeature.data.user.file[[1]])) {
cur.biofeat <- i
cur.biofeat.data <- split.biofeature.data.user.file[[1]][i]
cur.biofeat.type <- split.biofeature.data.user.type[[1]][i]
if(cur.biofeat.type == "GeneRegion"){
track.biofeat <- GeneRegionTrack(range=cur.biofeat.data, genome=config.var$genome, chromosome=gbl.var$mydata.chr)
}else if (cur.biofeat.type == "Annotation") {
track.biofeat <- AnnotationTrack(range=cur.biofeat.data, genome=config.var$genome, chromosome=gbl.var$mydata.chr)
}else if (cur.biofeat.type == "DATA") {
num.data <- num.data + 1
cur.biofeat.type.plot <- split.biofeature.data.user.type.plot[[1]][num.data]
track.biofeat <- DataTrack(range=cur.biofeat.data, genome=config.var$genome, type=cur.biofeat.type.plot, chromosome=gbl.var$mydata.chr)
}else {
dev.off()
stop("TYPE of TRACK UNKNOWN \n")
}
if (cur.biofeat == 0){
listtracks_user=list(track.biofeat)
}else{
listtracks_user = c(listtracks_user, track.biofeat)
}
}
gbl.var$listtracks_user <- c(listtracks_user)
}
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.TRACKS.USER\n")
return(gbl.var)
}
#-------------------CREATE TRACKS for WEB PAGE----------------------------
create.tracks.web <- function(config.var,gbl.var) {
#DEBUG STATEMENT
if (config.var$verbose) cat("START CREATE.TRACKS.WEB\n")
listtracks_gviz <-list()
# if (config.var$verbose) cat("test",is.hash(gbl.var$split.list.tracks))
#---- genome Axis
if(has.key("genomeAxis", gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw genomeAxis\n")
gtrack <- GenomeAxisTrack()
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(gtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,gtrack)
}
}
#--- GENES ENSEMBL
if(has.key("geneENSEMBL", gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw geneENSEMBL\n")
ENSEMBLtrack <- genes_ENSEMBL(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x,showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(ENSEMBLtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,ENSEMBLtrack)
}
}
#--- transcript ENSEMBL
if(has.key("transcriptENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw transcriptENSEMBL\n")
tENSEMBLtrack <- transcript_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x,showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(tENSEMBLtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,tENSEMBLtrack)
}
}
#--- Known gene UCSC
if(has.key("genesUCSC",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw genesUCSC\n")
dnasetrack<-knownGenes_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,
gbl.var$max.x,showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(dnasetrack)
} else {
listtracks_gviz <- c(listtracks_gviz,dnasetrack)
}
}
#--- ref gene UCSC
if(has.key("refgenesUCSC",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw ref genes UCSC\n")
refGenestrack<-refGenes_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x,
IdType = "Ref", showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(refGenestrack)
} else {
listtracks_gviz <- c(listtracks_gviz,refGenestrack)
}
}
#------ xeno ref
if(has.key("xenogenesUCSC",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw xenogenesUCSC\n")
gctrack <-xenorefGenes_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,
gbl.var$max.x,showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(gctrack)
} else {
listtracks_gviz <- c(listtracks_gviz,gctrack)
}
}
#--- CG Island
if(has.key("CGI",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw CGI\n")
cgitrack<-cpgIslands_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(cgitrack)
} else {
listtracks_gviz <- c(listtracks_gviz,cgitrack)
}
}
#--- ChromatinHMM
if(has.key("ChromHMM",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw ChromHMM\n")
chromatintrack <- chromatinHMMAll_UCSC(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x,gbl.var$mySession,
color= 'coMET',
config.var$pattern.regulation)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(chromatintrack)
} else {
listtracks_gviz <- c(listtracks_gviz,chromatintrack)
}
}
#--- Broad Histone
if(has.key("BroadHistone",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw BroadHistone\n")
chromatintrack <- HistoneAll_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x,
gbl.var$mySession,track.name="Broad histone",
pattern=config.var$pattern.regulation)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(chromatintrack)
} else {
listtracks_gviz <- c(listtracks_gviz,chromatintrack)
}
}
#--- DNAse
if(has.key("DNAse",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw DNAse\n")
dnasetrack<-DNAse_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,
gbl.var$max.x,gbl.var$mySession)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(dnasetrack)
} else {
listtracks_gviz <- c(listtracks_gviz,dnasetrack)
}
}
#---- Regulation (hg19)
if(has.key("RegENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw RegENSEMBL\n")
regtrack<-regulationBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(regtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,regtrack)
}
}
#---- BindingMotifENSEMBL
if(has.key("BindingMotifENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw BindingMotifENSEMBL\n")
BMtrack<-bindingMotifsBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(BMtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,BMtrack)
}
}
#---- regulatoryFeaturesENSEMBL
if(has.key("otherRegulatoryENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw otherRegulatoryENSEMBL\n")
ORtrack<-otherRegulatoryRegionsBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(ORtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,ORtrack)
}
}
#---- regulatoryFeaturesENSEMBL
if(has.key("regulatoryEvidenceENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw regulatoryFeaturesENSEMBL\n")
REtrack<-regulatoryEvidenceBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(REtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,REtrack)
}
}
#---- regulatoryFeaturesENSEMBL
if(has.key("regulatoryFeaturesENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw regulatoryFeaturesENSEMBL\n")
RFtrack<-regulatoryFeaturesBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(RFtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,RFtrack)
}
}
#---- regulatorySegmeENSEMBL
if(has.key("regulatorySegmeENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw regulatorySegmeENSEMBL\n")
RStrack<-regulatorySegmentsBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(RStrack)
} else {
listtracks_gviz <- c(listtracks_gviz,RStrack)
}
}
#---- miRNA
if(has.key("miRNAENSEMBL",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw miRNAENSEMBL\n")
mirnatrack<-miRNATargetRegionsBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,
gbl.var$min.x,
gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(mirnatrack)
} else {
listtracks_gviz <- c(listtracks_gviz,mirnatrack)
}
}
#---- structural variation
if(has.key("SNPstru",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw SNPstru\n")
structrack<-structureBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x,"*",
config.var$DATASET.STRU)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(structrack)
} else {
listtracks_gviz <- c(listtracks_gviz,structrack)
}
}
#---- stomatic structural variation
if(has.key("SNPstrustoma",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw SNPstrustoma\n")
structrack<-structureBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x,"*",
config.var$DATASET.STRU.STOMA)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(structrack)
} else {
listtracks_gviz <- c(listtracks_gviz,structrack)
}
}
#---- SNP stomatic cell
if(has.key("SNPstoma",gbl.var$split.list.tracks)) {
if (config.var$verbose) cat("Draw SNPstoma\n")
snpstomaENSEMBLtrack<-snpBiomart_ENSEMBL(config.var$genome,
gbl.var$mydata.chr,gbl.var$min.x,gbl.var$max.x,
config.var$DATASET.SNP.STOMA,
title="Stomatic Short Variation")
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(snpstomaENSEMBLtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,snpstomaENSEMBLtrack)
}
}
#---- SNP
if(has.key("SNP",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw SNP\n")
snptrack <- snpLocations_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,
gbl.var$max.x,config.var$VERSION.DBSNP)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(snptrack)
} else {
listtracks_gviz <- c(listtracks_gviz,snptrack)
}
}
#------ Imprinted genes
if(has.key("ImprintedtissuesGenes",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw tissue-specific imprinted genes \n")
imprintedtrack <-imprintedGenes_GTEx(gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x, tissues="all",
classification="all",showId=FALSE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(imprintedtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,imprintedtrack)
}
}
#------ COSMIC
if(has.key("COSMIC",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw COSMIC\n")
cosmictrack <-COSMIC_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x,showId=FALSE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(cosmictrack)
} else {
listtracks_gviz <- c(listtracks_gviz,cosmictrack)
}
}
#------ GAD
if(has.key("GAD",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw GAD\n")
iscatrack <-GAD_UCSC(config.var$genome,gbl.var$mydata.chr,gbl.var$min.x,
gbl.var$max.x,showId=FALSE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(iscatrack)
} else {
listtracks_gviz <- c(listtracks_gviz,iscatrack)
}
}
#------ clinic Variant
if(has.key("ClinVar",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw ClinVar\n")
clinVariant<-ClinVarMain_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(clinVariant)
} else {
listtracks_gviz <- c(listtracks_gviz,clinVariant)
}
}
if(has.key("ClinVarCNV",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw ClinVarCNV\n")
clinCNV<-ClinVarCnv_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(clinCNV)
} else {
listtracks_gviz <- c(listtracks_gviz,clinCNV)
}
}
#------ GWAS Variant
if(has.key("GWAS",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw GWAS\n")
gwastrack <-GWAScatalog_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(gwastrack)
} else {
listtracks_gviz <- c(listtracks_gviz,gwastrack)
}
}
#------ GeneReviews
if(has.key("GeneReviews",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw GeneReviews\n")
geneRtrack <-GeneReviews_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(geneRtrack)
} else {
listtracks_gviz <- c(listtracks_gviz,geneRtrack)
}
}
#------ GC content
if(has.key("GCcontent",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw GCcontent\n")
gctrack <-gcContent_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(gctrack)
} else {
listtracks_gviz <- c(listtracks_gviz,gctrack)
}
}
#------ Repeat element
if(has.key("RepeatElt",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw RepeatElt\n")
reptrack <-repeatMasker_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x,showId=TRUE)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(reptrack)
} else {
listtracks_gviz <- c(listtracks_gviz,reptrack)
}
}
#------ Segmental duplication
if(has.key("SegDuplication",gbl.var$split.list.tracks) ){
if (config.var$verbose) cat("Draw SegDuplication\n")
segDuptrack <-segmentalDups_UCSC(config.var$genome,gbl.var$mydata.chr,
gbl.var$min.x,gbl.var$max.x)
if(length(listtracks_gviz) == 0) {
listtracks_gviz <- list(segDuptrack)
} else {
listtracks_gviz <- c(listtracks_gviz,segDuptrack)
}
}
#------ BioUSER
if(!is.null(config.var$biofeat.user.file)){
if (config.var$verbose) cat("Draw BioUser\n")
if(length(gbl.var$listtracks_user) == 0) {
listtracks_gviz <- gbl.var$listtracks_user
} else {
listtracks_gviz <- c(listtracks_gviz,gbl.var$listtracks_user)
}
}
# if (config.var$zoom) {
# listtracks_gviz=c(list(tENSEMBLtrack,cgitrack),chromatintrack,dnasetrack,regtrack,snptrack)
# }else {
# listtracks_gviz=c(list(ENSEMBLtrack,cgitrack),chromatintrack,dnasetrack,regtrack,snptrack)
# }
gbl.var$listtracks_gviz <- listtracks_gviz
#DEBUG STATEMENT
if (config.var$verbose) cat("FINISH CREATE.TRACKS.WEB\n")
return(gbl.var)
}
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