R/internal_graphicModule.R
In mixOmicsTeam/mixOmics: Omics Data Integration Project
Defines functions
internal_graphicModule
################################################################################
# Author:
# Florian Rohart,
#
# created: 16-03-2016
# last modified: 24-08-2016
#
# Copyright (C) 2016
#
# 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
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
################################################################################
# -----------------------------------------------------------------------------
# Internal helpers functions to run "plotIndiv" functions
# -----------------------------------------------------------------------------
# df: data frame with all the information needed: coordinates (x,y,z),
# grouping factor 'group', 'Block' that indicates the block,
# names (ind.names), 'pch', 'cex' or each point,
# 'col.per.group' that gives the color of each point,
# 'pch.legend' that gives the pch of each point for the legend (same as pch?)
# as well as: x0 and y0 if plot centroid==TRUE
# centroid
# star
# ellipse
# df.ellipse
# xlim
# ylim
# title
# X.label
# Y.label
# legend
# display.names
internal_graphicModule <-
function(df,
centroid,
col.per.group,
title,
X.label,
Y.label,
Z.label,
xlim,
ylim,
zlim,
class.object,
display.names,
legend,
abline,
star,
ellipse,
df.ellipse,
style,
layout=NULL,
#missing.col,
axes.box,
study.levels,
plot_parameters,
alpha,
background = NULL)
{
object.pls = c("mixo_pls", "mixo_spls", "mixo_mlspls", "rcc")
object.pca = c("ipca", "sipca", "pca", "spca", "prcomp")
object.blocks = c("sgcca", "rgcca")
object.mint = c("mint.pls", "mint.spls", "mint.plsda", "mint.splsda")
#class.object=class(object)
# to satisfy R CMD check that doesn't recognise x, y and group (in aes)
x = y = group = pch = studyname = pch.levels = Var1 = Var2 = NULL
size.title = plot_parameters$size.title
size.subtitle = plot_parameters$size.subtitle
size.xlabel = plot_parameters$size.xlabel
size.ylabel = plot_parameters$size.ylabel
size.axis = plot_parameters$size.axis
size.legend = plot_parameters$size.legend
size.legend.title = plot_parameters$size.legend.title
legend.title = plot_parameters$legend.title
legend.title.pch = plot_parameters$legend.title.pch
legend.position = plot_parameters$legend.position
point.lwd = plot_parameters$point.lwd
# check whether pch and group are the same factors,
# otherwise we need two legends
group.pch = "same"
temp = table(df$group, df$pch)
# if factors are the same, there should be only one value
# different from 0 per column/row
# if pch is same factor as color, then same legend
a = NULL
for(i in 1:nrow(temp))
{
a = c(a, sum(temp[i,]!=0))
}
if(sum(a) != nrow(temp))
{
group.pch = "different"
} else {
a = NULL
for(j in 1:ncol(temp))
{
a = c(a, sum(temp[,j]!=0))
}
if(sum(a) != ncol(temp))
group.pch = "different"
}
# removed code to force as.character below because pch.levels should never be reordered, always the same (1, 2, 3, 4..) and they should always match the order of df$group levels
df$pch.levels = factor(as.numeric(df$pch.levels))
#df$pch.levels = factor(as.character(df$pch.levels)) #forced to be character,
# so that the order of the levels is the same all the time
# (1, 10, 11, 12, 2, 3...), instead of changing between ggplot2 and
# the rest
# df$pch.levels is sorted in the legend, we need to have the df$pch in the
# same order so that points/legend are matching
a=sort(unique(as.numeric(df$pch.levels)),index.return=TRUE)
# unique(df$pch.levels)[a$ix] is ordered
values.pch = unique(df$pch) [a$ix]
#values.pch = unique(df$pch)[match(unique(df$pch.levels),
# sort(levels(df$pch.levels)))]#as.numeric(levels(df$pch.levels))
#unique(df$pch)[as.numeric(unique(df$pch.levels))]
# makes pch and pch.levels correspond
#df$pch = factor(df$pch) #number or names
# shape in ggplot is ordered by the levels of pch.levels:
# levels(factor(as.character(df$pch.levels)))
# override if only one pch
if(nlevels(factor(df$pch)) == 1)
group.pch = "same"
#save(list=ls(),file="temp.Rdata")
#-- Start: ggplot2
if (style == "ggplot2")
{
nResp = nlevels(df$Block)
if (is.null(layout))
{
nRows = min(c(3, ceiling(nResp/2)))
nCols = min(c(3, ceiling(nResp/nRows)))
layout = c(nRows, nCols)
} else {
if (length(layout) != 2 || !is.numeric(layout) ||
any(is.na(layout)))
stop("'layout' must be a numeric vector of length 2.")
nRows = layout[1]
nCols = layout[2]
}
#note: at this present time, ggplot2 does not allow xlim to be changed
# per subplot, so cannot use xlim properly
#-- Initialise ggplot2
p = ggplot(df, aes(x = x, y = y, color = group, shape = pch.levels)) +
labs(title=title, x = X.label, y = Y.label) +
theme_bw() + theme(strip.text = element_text(size = size.subtitle,
face = "bold"))
if(!is.null(background))
{
for(i in 1:length(background))
{
if(!is.null(background[[i]]))
background[[i]]=data.frame(id=i,col=names(background)[i],
background[[i]])
}
background = do.call(rbind,background)
p = p+geom_polygon(data = background,aes(x=Var1, y=Var2,
fill = col), inherit.aes = FALSE, show.legend
=FALSE)
col.vals <- as.character(unique(background$col))
names(col.vals) <- col.vals
p = p + scale_fill_manual(values =
col.vals)
if(is.null(xlim))# we choose xlim that fits the points,
# and not the background
xlim = range(df$x)
if(is.null(ylim))# we choose ylim that fits the points,
# and not the background
ylim = range(df$y)
}
#-- Display sample or row.names
for (i in levels(df$group))
{
if(display.names)
{
p = p + geom_point(data = subset(df, df$group == i),
size = 0, shape = 0)
} else {
p = p + geom_point(data = subset(df, df$group == i),
size = subset(df, df$group == i)$cex[1], stroke = point.lwd)
}
if (centroid == TRUE)
{
p = p + geom_point(data = subset(df[, c("col", "x0", "y0",
"Block", "cex", "pch", "group")], df$group == i),
aes(x=x0,y=y0), size = 0, shape = 0)
}
}
#-- Modify scale colour - Change X/Ylabel - split plots into Blocks
## order of 'col.per.group' will correspond to order of levels in 'df$group'
p = p + scale_color_manual(values = col.per.group, name = legend.title)
if(group.pch == "same")
{
p = p + scale_shape_manual(values = values.pch,
name = legend.title, labels = levels(factor(df$group)),
guide = "none")
#match(..) reorder the values as the values of pch.levels,
#if there's more than 10 levels, R/ggplot orders characters
#different than values 1, 10, 11, 2, 3, etc
} else {
# if pch different factor, then second legend
p = p + scale_shape_manual(values = values.pch,
name = legend.title.pch, labels = values.pch)
}
p = p + #labs(list(title = title, x = X.label, y = Y.label)) +
facet_wrap(~ Block, ncol = nCols, scales = "free", as.table = TRUE)
#as.table to plot in the same order as the factor
p = p + theme(plot.title=element_text(size=size.title),
axis.title.x=element_text(size=size.xlabel),
axis.title.y=element_text(size=size.ylabel),
axis.text=element_text(size=size.axis))# bigger title
#-- xlim, ylim
p = p + coord_cartesian(xlim=xlim,ylim=ylim)
#-- color samples according to col
for (i in unique(df$col))
{
for(j in 1:nlevels(df$Block))
{
if (display.names)
{
p = p +geom_point(data = subset(df, col == i &
df$Block == levels(df$Block)[j]),size = 0, shape = 0,
color = unique(df[df$col == i & df$Block ==
levels(df$Block)[j], ]$col))+
geom_text(data = subset(df, col == i & df$Block ==
levels(df$Block)[j]),
aes(label = names),
color = df[df$col == i & df$Block ==
levels(df$Block)[j], ]$col,
size = df[df$col == i & df$Block ==
levels(df$Block)[j], ]$cex,show.legend = FALSE)
}
if (centroid == TRUE)
{
p = p + geom_point(data = subset(df[, c("col", "x0", "y0",
"Block", "cex", "pch", "group")], col == i),
aes(x = x0, y = y0),
color = unique(df[df$col == i &
df$Block == levels(df$Block)[1], ]$col),
size = unique(df[df$col == i &
df$Block == levels(df$Block)[1], ]$cex),
shape = 8, stroke = point.lwd)
}
}
}
#-- Legend
if (!legend)
{
p = p + theme(legend.position="none")
} else if(group.pch == "same") {
if (display.names | any(class.object%in%object.mint) ) {
group.shape <- 19
} else {
# keep order of pch.levels the same
group.shape <- as.numeric(levels(df$pch.levels))
if (length(group.shape) > 1)
{
# keep order of df$group levels the same
names(group.shape) <- levels(df$pch.legend)
}
}
p = p + guides(color =
guide_legend(override.aes =
list(
shape = group.shape,
size = 3,
stroke = point.lwd
))) +
theme(legend.title=element_text(size=size.legend.title),
legend.text=element_text(size=size.legend)) +
theme(legend.position=legend.position)
} else if(group.pch == "different") {
p = p + guides(shape = guide_legend(override.aes =
list(size=3, stroke=point.lwd)))
}
#-- abline
if (abline)
p = p + geom_vline(aes(xintercept = 0), linetype = 2,
colour = "darkgrey") + geom_hline(aes(yintercept = 0),
linetype = 2, colour = "darkgrey")
#-- star
if (star == TRUE)
{
for (i in 1 : nlevels(df$group))
{
p = p + geom_segment(data = subset(df, group ==
levels(df$group)[i]),
aes(x = x0, y = y0, xend = x, yend = y),
#label = "Block"),
color = unique(col.per.group)[i],size = point.lwd)
}
}
#-- ellipse
if (ellipse == TRUE)
{
for (i in 1 : nlevels(df$group))
{
if( !is.na(match(paste0("Col", 2*(i - 1) + 1),
colnames(df.ellipse))))
{
p = p + geom_path(data = df.ellipse,
aes(x = .data[[paste0("Col", 2*(i - 1) + 1)]],
y = .data[[paste0("Col", 2 * i)]],
group = NULL),
color = unique(col.per.group)[i],
linewidth = point.lwd,
inherit.aes = FALSE)
}
}
}
plot(p)
}
#-- End: ggplot2
#-- Start: ggplot2
if (style=="ggplot2-MINT")
{
nResp = nlevels(df$Block)
if (is.null(layout))
{
nRows = min(c(3, ceiling(nResp/2)))
nCols = min(c(3, ceiling(nResp/nRows)))
layout = c(nRows, nCols)
} else {
if (length(layout) != 2 || !is.numeric(layout) ||
any(is.na(layout)))
stop("'layout' must be a numeric vector of length 2.")
nRows = layout[1]
nCols = layout[2]
}
#note: at this present time, ggplot2 does not allow xlim to be
# changed per subplot, so cannot use xlim properly
df$studyname = factor(df$pch, labels = study.levels)
#-- Initialise ggplot2
p = ggplot(df, aes(x = x, y = y, color = group, shape = studyname)) +
labs(title=title, x = X.label, y = Y.label) +
theme_bw() + theme(strip.text = element_text(size = size.subtitle,
face = "bold"))
#-- Display sample or row.names
for (i in levels(df$group))
{
p = p + geom_point(data = subset(df, df$group == i),
size = subset(df, df$group == i)$cex[1], stroke = point.lwd)
}
#-- Modify scale colour - Change X/Ylabel - split plots into Blocks
p = p + scale_colour_manual(values = unique(col.per.group),
name = legend.title) +
labs(shape = "Study")#levels(object$study)[study.ind])
p = p + scale_shape_manual(values = as.numeric(levels(factor(df$pch))))
# replace the shape/pch by the input, it's converted by default to
# 1,2,3.. by ggplots
p = p + #labs(list(title = title, x = X.label, y = Y.label)) +
facet_wrap(~ Block, ncol = nCols, scales = "free", as.table = TRUE)
#as.table to plot in the same order as the factor
p = p + theme(plot.title = element_text(size=size.title),
axis.title.x = element_text(size=size.xlabel),
axis.title.y = element_text(size = size.ylabel),
axis.text = element_text(size = size.axis))# bigger title
#-- xlim, ylim
p = p + coord_cartesian(xlim = xlim, ylim = ylim)
#-- Legend
if (!legend)
{
p = p + theme(legend.position="none")
}else{
p = p + guides(colour = guide_legend(override.aes =
list(size = unique(df$cex)))) +
theme(legend.title = element_text(size = size.legend.title),
legend.text = element_text(size = size.legend))+
theme(legend.position = legend.position)
}
#-- abline
if (abline)
p = p + geom_vline(aes(xintercept = 0), linetype = 2,
colour = "darkgrey") + geom_hline(aes(yintercept = 0),
linetype = 2,colour = "darkgrey")
#-- centroid
if (centroid == TRUE) #only when one block
{
for (i in levels(df$group))
{
p = p + geom_point(data = subset(df, df$group == i),
aes(x = x0, y = y0),
color = subset(df, df$group == i)$col[1],
size = subset(df, df$group == i)$cex[1],
shape = 8, stroke = point.lwd)
}
}
#-- star
if (star == TRUE) #only when one block
{
for (i in 1 : nlevels(df$group))
{
p = p + geom_segment(data = subset(df, group ==
levels(df$group)[i]),
aes(x = x0, y = y0, xend = x, yend = y),
#label = "Block"),
color = unique(col.per.group)[i],size = point.lwd)
}
}
#-- ellipse
if (ellipse == TRUE) #only when one block
{
for (i in 1 : nlevels(df$group))
{
p = p + geom_path(data = df.ellipse,
aes(x = .data[[paste0("Col", 2*(i - 1) + 1)]],
y = .data[[paste0("Col", 2 * i)]],
group = NULL),
color = unique(col.per.group)[i],
linewidth = point.lwd,
inherit.aes = FALSE)
}
}
if(!is.null(background))
{
for(i in 1:length(background))
{
if(!is.null(background[[i]]))
background[[i]]=data.frame(id=i,col=names(background)[i],
background[[i]])
}
background = do.call(rbind,background)
p = p+geom_polygon(data = background,aes(x=Var1, y=Var2,
fill = col), inherit.aes = FALSE, show.legend
=FALSE)
col.vals <- as.character(unique(background$col))
names(col.vals) <- col.vals
p = p + scale_fill_manual(values =
col.vals)
if(is.null(xlim))
xlim = range(df$x)
if(is.null(ylim))
ylim = range(df$y)
}
plot(p)
}
#-- End: ggplot2
if (style=="lattice")
{
#-- Start: Lattice
p = xyplot(y ~ x | Block, data = df, xlab = list(label=X.label,
cex=size.xlabel), ylab = list(label=Y.label,cex=size.ylabel),
main = list(label = title, cex = size.title), as.table = TRUE,
#as.table plot in order
groups = if (display.names) {names} else {group},
scales= list(x = list(relation = "free", limits = xlim,cex=size.axis),
y = list(relation = "free", limits = ylim,cex=size.axis)),
#-- Legend
key = if(legend == TRUE)
{
if (!any(class.object%in%object.mint))
{
if(group.pch == "same")
{
list(space = legend.position, title = legend.title,
cex.title = size.legend.title,
point = list(col = col.per.group),cex=size.legend,
pch = if(display.names | any(class.object%in%object.mint))
{16} else unique(df$pch.legend),text =
list(levels(df$group)))
} else {
list(space = legend.position, cex.title = size.legend.title,
point = list(
col = c(NA, col.per.group, NA, NA, rep("black",
nlevels(df$pch.levels)))),
cex = c(size.legend.title, rep(size.legend,
length(col.per.group)), size.legend, size.legend.title,
rep(size.legend,nlevels(factor(df$pch)))),
pch = c(NA, rep(16, length(col.per.group)), NA, NA,
values.pch),
text = list(outcome = c(legend.title, levels(df$group),
"", legend.title.pch, levels(df$pch.levels)))
)
}
} else {#we add the shape legend
list(space = legend.position, cex.title = size.legend.title,
point = list(
col = c(NA, col.per.group, NA, NA, rep("black",
length(study.levels)))),
cex = c(size.legend.title, rep(size.legend,
length(col.per.group)), size.legend, size.legend.title,
rep(size.legend,nlevels(factor(df$pch)))),
pch = c(NA, rep(16, length(col.per.group)), NA, NA,
as.numeric(levels(factor(df$pch)))),
text = list(outcome = c(legend.title, levels(df$group),
"", "Study", study.levels))
)
}
} else {
NULL
},
panel = function(x, y, subscripts, groups, display = display.names,...)
{
#-- Abline
if (abline)
{
panel.abline(v = 0, lty = 2, col = "darkgrey")
panel.abline(h = 0, lty = 2, col = "darkgrey")
}
#-- Background
if (!is.null(background)) # only first block: plsda and splsda
{
for (i in 1 : length(background))
panel.polygon(background[[i]], col = names(background)[i],
border=NA)
}
#-- Display sample or row.names
for (i in 1 : nlevels(df$group))
{
if (display)
{
ltext(x = df$x[df$group == levels(df$group)[i]],
y = df$y[df$group == levels(df$group)[i]],
labels = groups[subscripts & df$group ==
levels(df$group)[i]], col = "white", cex = 0)
} else {
lpoints(x = df$x[df$group == levels(df$group)[i]],
y = df$y[df$group == levels(df$group)[i]],
col = "white", cex = 0, pch = 0)
}
}
#-- color samples according to col
for (i in unique(df$col))
{
if (display)
{
ltext(x = df$x[subscripts] [df$col[subscripts] == i],
y = df$y[subscripts] [df$col[subscripts] == i],
labels = groups[subscripts & df$col == i],
col = df[df$col == i, ]$col, cex =
df$cex[subscripts][df$col[subscripts] == i])
} else {
lpoints(x = df$x[subscripts] [df$col[subscripts] == i],
y = df$y[subscripts] [df$col[subscripts] == i],
col = df[df$col == i, ]$col,
cex = df$cex[subscripts][df$col[subscripts] == i],
pch = df$pch[subscripts][df$col[subscripts] == i])
}
}
}
)
print(p)
#the lattice plot needs to be printed in order to display the ellipse(s)
#-- centroid
if (centroid)
{
panels = trellis.currentLayout(which = "panel")
for (k in 1 : nlevels(df$Block))
{
other = df$Block %in% levels(df$Block)[k]
ind = which(panels == k, arr.ind = TRUE)
trellis.focus("panel", ind[2], ind[1], highlight = FALSE)
for (i in 1 : nlevels(df$group))
{
x0 = mean(df[other & df$group == levels(df$group)[i], ]$x)
y0 = mean(df[other & df$group == levels(df$group)[i], ]$y)
panel.points(x = x0, y = y0, col = unique(col.per.group)[i],
pch = 8, cex = df[other & df$group ==
levels(df$group)[i], ]$cex)
}
}
trellis.unfocus()
}
#-- star
if (star)
{
panels = trellis.currentLayout(which = "panel")
for (k in 1 : nlevels(df$Block))
{
other = df$Block %in% levels(df$Block)[k]
ind = which(panels == k, arr.ind = TRUE)
trellis.focus("panel", ind[2], ind[1], highlight = FALSE)
for (i in 1 : nlevels(df$group))
{
for (q in 1: length(df[other & df$group ==
levels(df$group)[i] , "x"]))
{
x0 = mean(df[other & df$group == levels(df$group)[i] ,
]$x)
y0 = mean(df[other & df$group == levels(df$group)[i] ,
]$y)
panel.segments(x0, y0, df[other & df$group ==
levels(df$group)[i], ]$x[q],
df[other & df$group == levels(df$group)[i], ]$y[q],
col = unique(col.per.group)[i], cex = df[other &
df$group == levels(df$group)[i], ]$cex,
pch = df[other & df$group == levels(df$group)[i], ]$pch)
}
}
}
trellis.unfocus()
}
#-- ellipse
if (ellipse)
{
panels = trellis.currentLayout(which = "panel")
for (k in 1 : nlevels(df$Block))
{
other.ellipse = df.ellipse$Block %in% levels(df$Block)[k]
ind = which(panels == k, arr.ind = TRUE)
trellis.focus("panel",ind[2], ind[1], highlight = FALSE)
for (i in 1 : nlevels(df$group))
{
panel.lines(x = df.ellipse[other.ellipse, paste0("Col",
2*(i - 1) + 1)],
y = df.ellipse[other.ellipse, paste0("Col", 2 * i)],
col = unique(col.per.group)[i])
}
}
trellis.unfocus()
}
}
#-- End: Lattice
if (style=="graphics")
{
#-- Start: graphics
#df$pch = as.numeric(df$pch) #number or names
opar = par(c("mai","mar","usr","cxy","xaxp","yaxp"))
reset.mfrow = FALSE
# if set to TRUE, the algorithm ends up with par(mfrow=reset.mfrow)
#-- Define layout
nResp = nlevels(df$Block)
if (is.null(layout))
{
# check if there are enough plots in mfrow
omfrow = par("mfrow")
available.plots = prod(omfrow)
if (available.plots<nResp)
# if not enough plots available, we create our new plot
{
nRows = min(c(3, ceiling(nResp/2)))
nCols = min(c(3, ceiling(nResp/nRows)))
layout = c(nRows, nCols)
par(mfrow = layout)
if (nRows * nCols < nResp)
devAskNewPage(TRUE)
reset.mfrow=TRUE # we changed mfrow to suits our needs,
#so we reset it at the end
}
} else {
if (length(layout) != 2 || !is.numeric(layout) ||
any(is.na(layout)))
stop("'layout' must be a numeric vector of length 2.")
nRows = layout[1]
nCols = layout[2]
par(mfrow = layout)
if (nRows * nCols < nResp)
devAskNewPage(TRUE)
}
for (k in 1 : nlevels(df$Block))
{
if (legend & group.pch == "same")
{
par(mai=c(1.360000, 1.093333, 1.093333,
(max(strwidth(c(levels(df$group),legend.title),"inches"))) + 1),
xpd=TRUE)
} else if(legend & group.pch == "different") {
par(mai=c(1.360000, 1.093333, 1.093333,
(max(strwidth(c(levels(df$group),legend.title,legend.title.pch),
"inches"))) + 1), xpd=TRUE)
}
other = df$Block %in% levels(df$Block)[k]
plot(df[other, "x" ], df[other, "y" ],
type = "n", xlab = X.label, ylab = Y.label,
xlim = c(xlim[[k]][1], xlim[[k]][2]), ylim = c(ylim[[k]][1],
ylim[[k]][2]),
cex.axis = size.axis, cex.lab = size.xlabel, lwd = point.lwd)#,...)
#-- initialise plot
if (nlevels(df$Block) == 1 & !any(class.object%in%c(object.mint,
"sgcca", "rgcca")))
# avoid double title when only one block is plotted
{
titlemain = NULL
if (ellipse)
other.ellipse = TRUE
}else{
titlemain = levels(df$Block)[k]
if (ellipse)
other.ellipse = df.ellipse$Block %in% levels(df$Block)[k]
}
#add title of the 'blocks'
title(main = titlemain, line = 1, cex.main = size.subtitle)
#-- Display sample or row.names
for (i in 1 : nlevels(df$group))
{
if (display.names)
{
text(x = df[df$group == levels(df$group)[i] & other, "x"],
y = df[df$group == levels(df$group)[i] & other, "y"],
labels = df[df$group == levels(df$group)[i] & other,
"names"],
col = "white", cex = 0,lwd=point.lwd)#,...)
} else {
points(x = df[df$group == levels(df$group)[i] & other, "x"],
y = df[df$group == levels(df$group)[i] & other, "y"],
col = "white", cex = 0, pch = 0,lwd=point.lwd)#,...)
}
}
#-- color samples according to col
for (i in unique(df$col))
{
if (display.names)
{
text(x = df[df$col == i & other, "x"],
y = df[df$col == i & other, "y"],
labels = df[df$col == i & other, "names"],
col = df[df$col == i, ]$col, cex = df[df$col == i, ]$cex,
lwd=point.lwd)#,...)
} else {
points(x = df[df$col == i & other, "x"],
y = df[df$col == i & other, "y"],
col = df[df$col == i, ]$col,
cex = df[df$col == i, ]$cex,
pch = as.numeric(df[df$col == i, ]$pch.levels),
lwd=point.lwd)#,...)
}
}
if (legend & group.pch == "same")
{
pch.legend = NULL
for (i in 1:nlevels(df$group))
pch.legend = c(pch.legend, df[df$group == levels(df$group)[i],
]$pch)
legend(par()$usr[2]+0.1, par()$usr[4] -
(par()$usr[4]-par()$usr[3])/2, col = col.per.group,
legend = levels(df$group), pch = if(display.names) {16} else
unique(df$pch.legend), title = legend.title, cex = size.legend,
lty = 0,lwd = point.lwd)
} else if(legend & group.pch == "different") {
legend(par()$usr[2]+0.1, par()$usr[4] -
(par()$usr[4]-par()$usr[3])/2,
col = c(NA, col.per.group, NA, NA, rep("black",
nlevels(df$pch.levels))),
legend = c(legend.title, levels(df$group), "",
legend.title.pch, levels(df$pch.levels)),
pch = c(NA, rep(16, length(col.per.group)), NA, NA, values.pch),
cex = max(c(size.legend.title, size.legend)),
lty = 0,
lwd = point.lwd
)
}
if (legend)
par(xpd=FALSE) # so the abline does not go outside the plot
#-- Abline
if (abline)
abline(v = 0, h = 0, lty = 2,lwd=point.lwd)#,...)
#-- Star
if (star == TRUE)
{
for (i in 1 : nlevels(df$group))
{
x0 = mean(df[df$group == levels(df$group)[i] & other, "x"])
y0 = mean(df[df$group == levels(df$group)[i] & other, "y"])
for (q in 1: length(df[df$group == levels(df$group)[i] &
other, "x"]))
{
segments(x0, y0, df[df$group == levels(df$group)[i] &
other, "x"][q], df[df$group == levels(df$group)[i] &
other, "y"][q],
cex = df$df[df$group == levels(df$group)[i] & other,
"cex"], col = df[df$group == levels(df$group)[i] &
other, "col"], lwd = point.lwd)#,...)
}
}
}
#-- Centroid
if (centroid == TRUE)
{
for (i in 1 : nlevels(df$group))
{
x0 = mean(df[df$group == levels(df$group)[i] & other, "x"])
y0 = mean(df[df$group == levels(df$group)[i] & other, "y"])
points(cbind(x0,y0), pch = 8, cex = df$df[df$group ==
levels(df$group)[i] & other, "cex"],
col = unique(col.per.group)[i], lwd = point.lwd)#,...)
}
}
#-- Ellipse
if (ellipse == TRUE)
{
for (i in 1 : nlevels(df$group))
{
lines(x = df.ellipse[other.ellipse,
paste0("Col", 2*(i - 1) + 1)],
y = df.ellipse[other.ellipse, paste0("Col", 2 * i)],
col = unique(col.per.group)[i],lwd=point.lwd)#,...)
}
}
#-- Background
if (!is.null(background)) # only first block: plsda and splsda
{
for (i in 1 : length(background))
polygon(background[[i]], col = names(background)[i], border=NA)
}
if (nlevels(df$Block) == 1 & !any(class.object%in%c(object.mint,
"sgcca", "rgcca")))
# avoid double title when only one block is plotted
{
title(title, line = 1, cex.main = size.title)#,...)
} else {
title(title, outer=TRUE, line = -2,cex.main = size.title)#,...)
}
}
#par(opar)
#par(usr=opar["usr"])
#par(xaxp=opar["xaxp"])
#par(yaxp=opar["yaxp"])
#par(mai=opar["mai"])
if (reset.mfrow)
par(mfrow = omfrow)
#par(mar=opar["mar"])
}
#-- End: graphics
if (style=="3d")
{
if(requireNamespace("rgl") == FALSE)
stop("the rgl package is required for 3d plots")
#-- Start: 3d
for (k in 1 : nlevels(df$Block))
{
rgl::open3d()
rgl::par3d(windowRect = c(500, 30, 1100, 630))
Sys.sleep(0.1)
if (!is.null(title))
{
mat = matrix(1:2, 2)
rgl::layout3d(mat, heights = c(1, 10), model = "inherit")
rgl::next3d()
rgl::text3d(0, 0, 0, title)
rgl::next3d()
}
if(any(class.object %in% c("ipca", "sipca", "pca", "spca", "prcomp",
"mixo_splsda", "mixo_plsda", "mixo_mlsplsda")))
{
other = TRUE
if (ellipse)
other.ellipse = TRUE
} else {
other = df$Block %in% levels(df$Block)[k]
if (ellipse)
other.ellipse = df.ellipse$Block %in% levels(df$Block)[k]
}
rgl::par3d(userMatrix = rgl::rotationMatrix(pi/80, 1, -1/(100*pi), 0))
if (legend)
{
rgl::legend3d(x = "right",
legend = levels(df$group),
col = col.per.group,
pch = rep(16,length(unique(df$pch))),
pt.cex = unique(df$cex),
bty = "n")
}
#-- Display sample or row.names
for (i in unique(df$col))
{
if (display.names)
{
for (cex_i in unique(df[df$col == i, ]$cex))
{
ind = which(df[df$col == i, ]$cex == cex_i)
rgl::text3d(x = df[df$col == i & other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i & other, "z"][ind],
texts = df[df$col == i & other, "names"][ind],
color = df[df$col == i, ]$col[ind], cex = cex_i)
}
}else{
cex = 20*df[df$col == i, ]$cex
for (pch_i in unique(df[df$col == i, ]$pch))
{
ind = which(df[df$col == i, ]$pch == pch_i)
if(pch_i == "sphere")
{
for (cex_i in unique(df[df$col == i, ]$cex[ind]))
{
ind_cex = which(df[df$col == i, ]$cex[ind] ==
cex_i)
rgl::points3d(x = df[df$col == i &
other, "x"][ind][ind_cex],
y = df[df$col == i & other, "y"][ind][ind_cex],
z = df[df$col == i & other, "z"][ind][ind_cex],
col = df[df$col == i, ]$col[ind][ind_cex],
size = cex_i*20, radius = cex_i, add = TRUE)
}
} else if (pch_i == "tetra") {
rgl::shapelist3d(rgl::tetrahedron3d(), x = df[df$col == i &
other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i & other, "z"][ind],
col = df[df$col == i, ]$col[ind], size =
cex[ind]/25)
} else if (pch_i == "cube") {
rgl::shapelist3d(rgl::cube3d(),x = df[df$col == i &
other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i & other, "z"][ind],
col = df[df$col == i, ]$col[ind], size =
cex[ind]/30)
} else if (pch_i == "octa") {
rgl::shapelist3d(rgl::octahedron3d(), x = df[df$col == i &
other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i & other, "z"][ind],
col = df[df$col == i, ]$col[ind], size =
cex[ind]/17)
} else if (pch_i == "icosa") {
rgl::shapelist3d(rgl::icosahedron3d(), x = df[df$col == i &
other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i &other, "z"][ind],
col = df[df$col == i, ]$col[ind], size =
cex[ind]/20)
} else if (pch_i == "dodeca") {
rgl::shapelist3d(rgl::dodecahedron3d(), x = df[df$col == i &
other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i & other, "z"][ind],
col = df[df$col == i, ]$col[ind], size =
cex[ind]/20)
}
}
}
}
#-- Ellipse
if (ellipse)
{
coords = matrix(cbind(df[other, "x"],
df[other, "y"],
df[other,"z"]),ncol = 3)
centr.coords = apply(coords, 2, function(x)
tapply(x, df$group, mean))
if (length(unique(df$group)) == 1)
centr.coords = matrix(centr.coords, nrow=1)
rownames(centr.coords) = levels(df$group)
lg = levels(df$group)
for(i in 1:length(lg))
{
g = lg[i]
sel = df$group == g
s = cov(coords[sel, , drop = FALSE])
cc = centr.coords[i,]
# lines(ellipse(s, centre=cc), col=unique(col.per.group)[i])
rgl::shade3d(rgl::ellipse3d(s, centre = cc, level =
df.ellipse$ellipse.level[1]), col=unique(col.per.group)[i],
alpha = alpha)
}
}
#-- Centroid
if (centroid == TRUE)
{
for (i in 1 : nlevels(df$group))
{
x0 = mean(df[df$group == levels(df$group)[i] & other, "x"])
y0 = mean(df[df$group == levels(df$group)[i] & other, "y"])
z0 = mean(df[df$group == levels(df$group)[i] & other, "z"])
rgl::points3d(x=x0, y=y0,z=z0, cex=df$df[df$group ==
levels(df$group)[i] & other, "cex"], col =
unique(col.per.group)[i])
}
}
#-- Star
if (star == TRUE)
{
for (i in 1 : nlevels(df$group))
{
x0 = mean(df[df$group == levels(df$group)[i] & other, "x"])
y0 = mean(df[df$group == levels(df$group)[i] & other, "y"])
z0 = mean(df[df$group == levels(df$group)[i] & other, "z"])
for (q in 1: length(df[df$group == levels(df$group)[i] &
other, "x"]))
{
rgl::segments3d(x=c(x0, df[df$group == levels(df$group)[i] &
other, "x"][q]), y=c(y0,df[df$group ==
levels(df$group)[i] & other, "y"][q]),
z=c(z0, df[df$group == levels(df$group)[i] &
other, "z"][q]),
cex=df$df[df$group == levels(df$group)[i] &
other, "cex"], col=df[df$group == levels(df$group)[i] &
other, "col"])
}
}
}
#-- draws axes/box --#
if (axes.box == "box")
{
rgl::axes3d(marklen = 25)
rgl::box3d()
}
if (axes.box == "bbox")
{
rgl::bbox3d(color = c("#333377", "black"), emission = gray(0.5),
specular = gray(0.1), shininess = 5, alpha = 0.8, marklen = 25)
}
if (axes.box == "both")
{
rgl::axes3d(marklen = 25); rgl::box3d()
rgl::bbox3d(color = c("#333377", "black"), emission = gray(0.5),
specular = gray(0.1), shininess = 5, alpha = 0.8, marklen = 25)
}
#-- add axes labels --#
rgl::mtext3d(X.label, "x-+", line = 1)
rgl::mtext3d(Y.label, "y-+", line = 1.5)
rgl::mtext3d(Z.label, "z+-", line = 1)
if (! any(class.object%in% c("ipca", "sipca", "pca", "spca",
"prcomp", "mixo_splsda", "mixo_plsda", "mixo_mlsplsda")))
rgl::title3d(main = levels(df$Block)[k])
}
#-- output --#
return(invisible(cbind(df$x, df$y, df$z)))
}
if (style%in%c("graphics","3d"))
p = NULL
return(p)
}
mixOmicsTeam/mixOmics documentation built on Nov. 4, 2024, 8:56 a.m.
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Defines functions internal_graphicModule
################################################################################
# Author:
# Florian Rohart,
#
# created: 16-03-2016
# last modified: 24-08-2016
#
# Copyright (C) 2016
#
# 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
# Foundation, Inc., 59 Temple Place - Suite 330, Boston, MA 02111-1307, USA.
################################################################################
# -----------------------------------------------------------------------------
# Internal helpers functions to run "plotIndiv" functions
# -----------------------------------------------------------------------------
# df: data frame with all the information needed: coordinates (x,y,z),
# grouping factor 'group', 'Block' that indicates the block,
# names (ind.names), 'pch', 'cex' or each point,
# 'col.per.group' that gives the color of each point,
# 'pch.legend' that gives the pch of each point for the legend (same as pch?)
# as well as: x0 and y0 if plot centroid==TRUE
# centroid
# star
# ellipse
# df.ellipse
# xlim
# ylim
# title
# X.label
# Y.label
# legend
# display.names
internal_graphicModule <-
function(df,
centroid,
col.per.group,
title,
X.label,
Y.label,
Z.label,
xlim,
ylim,
zlim,
class.object,
display.names,
legend,
abline,
star,
ellipse,
df.ellipse,
style,
layout=NULL,
#missing.col,
axes.box,
study.levels,
plot_parameters,
alpha,
background = NULL)
{
object.pls = c("mixo_pls", "mixo_spls", "mixo_mlspls", "rcc")
object.pca = c("ipca", "sipca", "pca", "spca", "prcomp")
object.blocks = c("sgcca", "rgcca")
object.mint = c("mint.pls", "mint.spls", "mint.plsda", "mint.splsda")
#class.object=class(object)
# to satisfy R CMD check that doesn't recognise x, y and group (in aes)
x = y = group = pch = studyname = pch.levels = Var1 = Var2 = NULL
size.title = plot_parameters$size.title
size.subtitle = plot_parameters$size.subtitle
size.xlabel = plot_parameters$size.xlabel
size.ylabel = plot_parameters$size.ylabel
size.axis = plot_parameters$size.axis
size.legend = plot_parameters$size.legend
size.legend.title = plot_parameters$size.legend.title
legend.title = plot_parameters$legend.title
legend.title.pch = plot_parameters$legend.title.pch
legend.position = plot_parameters$legend.position
point.lwd = plot_parameters$point.lwd
# check whether pch and group are the same factors,
# otherwise we need two legends
group.pch = "same"
temp = table(df$group, df$pch)
# if factors are the same, there should be only one value
# different from 0 per column/row
# if pch is same factor as color, then same legend
a = NULL
for(i in 1:nrow(temp))
{
a = c(a, sum(temp[i,]!=0))
}
if(sum(a) != nrow(temp))
{
group.pch = "different"
} else {
a = NULL
for(j in 1:ncol(temp))
{
a = c(a, sum(temp[,j]!=0))
}
if(sum(a) != ncol(temp))
group.pch = "different"
}
# removed code to force as.character below because pch.levels should never be reordered, always the same (1, 2, 3, 4..) and they should always match the order of df$group levels
df$pch.levels = factor(as.numeric(df$pch.levels))
#df$pch.levels = factor(as.character(df$pch.levels)) #forced to be character,
# so that the order of the levels is the same all the time
# (1, 10, 11, 12, 2, 3...), instead of changing between ggplot2 and
# the rest
# df$pch.levels is sorted in the legend, we need to have the df$pch in the
# same order so that points/legend are matching
a=sort(unique(as.numeric(df$pch.levels)),index.return=TRUE)
# unique(df$pch.levels)[a$ix] is ordered
values.pch = unique(df$pch) [a$ix]
#values.pch = unique(df$pch)[match(unique(df$pch.levels),
# sort(levels(df$pch.levels)))]#as.numeric(levels(df$pch.levels))
#unique(df$pch)[as.numeric(unique(df$pch.levels))]
# makes pch and pch.levels correspond
#df$pch = factor(df$pch) #number or names
# shape in ggplot is ordered by the levels of pch.levels:
# levels(factor(as.character(df$pch.levels)))
# override if only one pch
if(nlevels(factor(df$pch)) == 1)
group.pch = "same"
#save(list=ls(),file="temp.Rdata")
#-- Start: ggplot2
if (style == "ggplot2")
{
nResp = nlevels(df$Block)
if (is.null(layout))
{
nRows = min(c(3, ceiling(nResp/2)))
nCols = min(c(3, ceiling(nResp/nRows)))
layout = c(nRows, nCols)
} else {
if (length(layout) != 2 || !is.numeric(layout) ||
any(is.na(layout)))
stop("'layout' must be a numeric vector of length 2.")
nRows = layout[1]
nCols = layout[2]
}
#note: at this present time, ggplot2 does not allow xlim to be changed
# per subplot, so cannot use xlim properly
#-- Initialise ggplot2
p = ggplot(df, aes(x = x, y = y, color = group, shape = pch.levels)) +
labs(title=title, x = X.label, y = Y.label) +
theme_bw() + theme(strip.text = element_text(size = size.subtitle,
face = "bold"))
if(!is.null(background))
{
for(i in 1:length(background))
{
if(!is.null(background[[i]]))
background[[i]]=data.frame(id=i,col=names(background)[i],
background[[i]])
}
background = do.call(rbind,background)
p = p+geom_polygon(data = background,aes(x=Var1, y=Var2,
fill = col), inherit.aes = FALSE, show.legend
=FALSE)
col.vals <- as.character(unique(background$col))
names(col.vals) <- col.vals
p = p + scale_fill_manual(values =
col.vals)
if(is.null(xlim))# we choose xlim that fits the points,
# and not the background
xlim = range(df$x)
if(is.null(ylim))# we choose ylim that fits the points,
# and not the background
ylim = range(df$y)
}
#-- Display sample or row.names
for (i in levels(df$group))
{
if(display.names)
{
p = p + geom_point(data = subset(df, df$group == i),
size = 0, shape = 0)
} else {
p = p + geom_point(data = subset(df, df$group == i),
size = subset(df, df$group == i)$cex[1], stroke = point.lwd)
}
if (centroid == TRUE)
{
p = p + geom_point(data = subset(df[, c("col", "x0", "y0",
"Block", "cex", "pch", "group")], df$group == i),
aes(x=x0,y=y0), size = 0, shape = 0)
}
}
#-- Modify scale colour - Change X/Ylabel - split plots into Blocks
## order of 'col.per.group' will correspond to order of levels in 'df$group'
p = p + scale_color_manual(values = col.per.group, name = legend.title)
if(group.pch == "same")
{
p = p + scale_shape_manual(values = values.pch,
name = legend.title, labels = levels(factor(df$group)),
guide = "none")
#match(..) reorder the values as the values of pch.levels,
#if there's more than 10 levels, R/ggplot orders characters
#different than values 1, 10, 11, 2, 3, etc
} else {
# if pch different factor, then second legend
p = p + scale_shape_manual(values = values.pch,
name = legend.title.pch, labels = values.pch)
}
p = p + #labs(list(title = title, x = X.label, y = Y.label)) +
facet_wrap(~ Block, ncol = nCols, scales = "free", as.table = TRUE)
#as.table to plot in the same order as the factor
p = p + theme(plot.title=element_text(size=size.title),
axis.title.x=element_text(size=size.xlabel),
axis.title.y=element_text(size=size.ylabel),
axis.text=element_text(size=size.axis))# bigger title
#-- xlim, ylim
p = p + coord_cartesian(xlim=xlim,ylim=ylim)
#-- color samples according to col
for (i in unique(df$col))
{
for(j in 1:nlevels(df$Block))
{
if (display.names)
{
p = p +geom_point(data = subset(df, col == i &
df$Block == levels(df$Block)[j]),size = 0, shape = 0,
color = unique(df[df$col == i & df$Block ==
levels(df$Block)[j], ]$col))+
geom_text(data = subset(df, col == i & df$Block ==
levels(df$Block)[j]),
aes(label = names),
color = df[df$col == i & df$Block ==
levels(df$Block)[j], ]$col,
size = df[df$col == i & df$Block ==
levels(df$Block)[j], ]$cex,show.legend = FALSE)
}
if (centroid == TRUE)
{
p = p + geom_point(data = subset(df[, c("col", "x0", "y0",
"Block", "cex", "pch", "group")], col == i),
aes(x = x0, y = y0),
color = unique(df[df$col == i &
df$Block == levels(df$Block)[1], ]$col),
size = unique(df[df$col == i &
df$Block == levels(df$Block)[1], ]$cex),
shape = 8, stroke = point.lwd)
}
}
}
#-- Legend
if (!legend)
{
p = p + theme(legend.position="none")
} else if(group.pch == "same") {
if (display.names | any(class.object%in%object.mint) ) {
group.shape <- 19
} else {
# keep order of pch.levels the same
group.shape <- as.numeric(levels(df$pch.levels))
if (length(group.shape) > 1)
{
# keep order of df$group levels the same
names(group.shape) <- levels(df$pch.legend)
}
}
p = p + guides(color =
guide_legend(override.aes =
list(
shape = group.shape,
size = 3,
stroke = point.lwd
))) +
theme(legend.title=element_text(size=size.legend.title),
legend.text=element_text(size=size.legend)) +
theme(legend.position=legend.position)
} else if(group.pch == "different") {
p = p + guides(shape = guide_legend(override.aes =
list(size=3, stroke=point.lwd)))
}
#-- abline
if (abline)
p = p + geom_vline(aes(xintercept = 0), linetype = 2,
colour = "darkgrey") + geom_hline(aes(yintercept = 0),
linetype = 2, colour = "darkgrey")
#-- star
if (star == TRUE)
{
for (i in 1 : nlevels(df$group))
{
p = p + geom_segment(data = subset(df, group ==
levels(df$group)[i]),
aes(x = x0, y = y0, xend = x, yend = y),
#label = "Block"),
color = unique(col.per.group)[i],size = point.lwd)
}
}
#-- ellipse
if (ellipse == TRUE)
{
for (i in 1 : nlevels(df$group))
{
if( !is.na(match(paste0("Col", 2*(i - 1) + 1),
colnames(df.ellipse))))
{
p = p + geom_path(data = df.ellipse,
aes(x = .data[[paste0("Col", 2*(i - 1) + 1)]],
y = .data[[paste0("Col", 2 * i)]],
group = NULL),
color = unique(col.per.group)[i],
linewidth = point.lwd,
inherit.aes = FALSE)
}
}
}
plot(p)
}
#-- End: ggplot2
#-- Start: ggplot2
if (style=="ggplot2-MINT")
{
nResp = nlevels(df$Block)
if (is.null(layout))
{
nRows = min(c(3, ceiling(nResp/2)))
nCols = min(c(3, ceiling(nResp/nRows)))
layout = c(nRows, nCols)
} else {
if (length(layout) != 2 || !is.numeric(layout) ||
any(is.na(layout)))
stop("'layout' must be a numeric vector of length 2.")
nRows = layout[1]
nCols = layout[2]
}
#note: at this present time, ggplot2 does not allow xlim to be
# changed per subplot, so cannot use xlim properly
df$studyname = factor(df$pch, labels = study.levels)
#-- Initialise ggplot2
p = ggplot(df, aes(x = x, y = y, color = group, shape = studyname)) +
labs(title=title, x = X.label, y = Y.label) +
theme_bw() + theme(strip.text = element_text(size = size.subtitle,
face = "bold"))
#-- Display sample or row.names
for (i in levels(df$group))
{
p = p + geom_point(data = subset(df, df$group == i),
size = subset(df, df$group == i)$cex[1], stroke = point.lwd)
}
#-- Modify scale colour - Change X/Ylabel - split plots into Blocks
p = p + scale_colour_manual(values = unique(col.per.group),
name = legend.title) +
labs(shape = "Study")#levels(object$study)[study.ind])
p = p + scale_shape_manual(values = as.numeric(levels(factor(df$pch))))
# replace the shape/pch by the input, it's converted by default to
# 1,2,3.. by ggplots
p = p + #labs(list(title = title, x = X.label, y = Y.label)) +
facet_wrap(~ Block, ncol = nCols, scales = "free", as.table = TRUE)
#as.table to plot in the same order as the factor
p = p + theme(plot.title = element_text(size=size.title),
axis.title.x = element_text(size=size.xlabel),
axis.title.y = element_text(size = size.ylabel),
axis.text = element_text(size = size.axis))# bigger title
#-- xlim, ylim
p = p + coord_cartesian(xlim = xlim, ylim = ylim)
#-- Legend
if (!legend)
{
p = p + theme(legend.position="none")
}else{
p = p + guides(colour = guide_legend(override.aes =
list(size = unique(df$cex)))) +
theme(legend.title = element_text(size = size.legend.title),
legend.text = element_text(size = size.legend))+
theme(legend.position = legend.position)
}
#-- abline
if (abline)
p = p + geom_vline(aes(xintercept = 0), linetype = 2,
colour = "darkgrey") + geom_hline(aes(yintercept = 0),
linetype = 2,colour = "darkgrey")
#-- centroid
if (centroid == TRUE) #only when one block
{
for (i in levels(df$group))
{
p = p + geom_point(data = subset(df, df$group == i),
aes(x = x0, y = y0),
color = subset(df, df$group == i)$col[1],
size = subset(df, df$group == i)$cex[1],
shape = 8, stroke = point.lwd)
}
}
#-- star
if (star == TRUE) #only when one block
{
for (i in 1 : nlevels(df$group))
{
p = p + geom_segment(data = subset(df, group ==
levels(df$group)[i]),
aes(x = x0, y = y0, xend = x, yend = y),
#label = "Block"),
color = unique(col.per.group)[i],size = point.lwd)
}
}
#-- ellipse
if (ellipse == TRUE) #only when one block
{
for (i in 1 : nlevels(df$group))
{
p = p + geom_path(data = df.ellipse,
aes(x = .data[[paste0("Col", 2*(i - 1) + 1)]],
y = .data[[paste0("Col", 2 * i)]],
group = NULL),
color = unique(col.per.group)[i],
linewidth = point.lwd,
inherit.aes = FALSE)
}
}
if(!is.null(background))
{
for(i in 1:length(background))
{
if(!is.null(background[[i]]))
background[[i]]=data.frame(id=i,col=names(background)[i],
background[[i]])
}
background = do.call(rbind,background)
p = p+geom_polygon(data = background,aes(x=Var1, y=Var2,
fill = col), inherit.aes = FALSE, show.legend
=FALSE)
col.vals <- as.character(unique(background$col))
names(col.vals) <- col.vals
p = p + scale_fill_manual(values =
col.vals)
if(is.null(xlim))
xlim = range(df$x)
if(is.null(ylim))
ylim = range(df$y)
}
plot(p)
}
#-- End: ggplot2
if (style=="lattice")
{
#-- Start: Lattice
p = xyplot(y ~ x | Block, data = df, xlab = list(label=X.label,
cex=size.xlabel), ylab = list(label=Y.label,cex=size.ylabel),
main = list(label = title, cex = size.title), as.table = TRUE,
#as.table plot in order
groups = if (display.names) {names} else {group},
scales= list(x = list(relation = "free", limits = xlim,cex=size.axis),
y = list(relation = "free", limits = ylim,cex=size.axis)),
#-- Legend
key = if(legend == TRUE)
{
if (!any(class.object%in%object.mint))
{
if(group.pch == "same")
{
list(space = legend.position, title = legend.title,
cex.title = size.legend.title,
point = list(col = col.per.group),cex=size.legend,
pch = if(display.names | any(class.object%in%object.mint))
{16} else unique(df$pch.legend),text =
list(levels(df$group)))
} else {
list(space = legend.position, cex.title = size.legend.title,
point = list(
col = c(NA, col.per.group, NA, NA, rep("black",
nlevels(df$pch.levels)))),
cex = c(size.legend.title, rep(size.legend,
length(col.per.group)), size.legend, size.legend.title,
rep(size.legend,nlevels(factor(df$pch)))),
pch = c(NA, rep(16, length(col.per.group)), NA, NA,
values.pch),
text = list(outcome = c(legend.title, levels(df$group),
"", legend.title.pch, levels(df$pch.levels)))
)
}
} else {#we add the shape legend
list(space = legend.position, cex.title = size.legend.title,
point = list(
col = c(NA, col.per.group, NA, NA, rep("black",
length(study.levels)))),
cex = c(size.legend.title, rep(size.legend,
length(col.per.group)), size.legend, size.legend.title,
rep(size.legend,nlevels(factor(df$pch)))),
pch = c(NA, rep(16, length(col.per.group)), NA, NA,
as.numeric(levels(factor(df$pch)))),
text = list(outcome = c(legend.title, levels(df$group),
"", "Study", study.levels))
)
}
} else {
NULL
},
panel = function(x, y, subscripts, groups, display = display.names,...)
{
#-- Abline
if (abline)
{
panel.abline(v = 0, lty = 2, col = "darkgrey")
panel.abline(h = 0, lty = 2, col = "darkgrey")
}
#-- Background
if (!is.null(background)) # only first block: plsda and splsda
{
for (i in 1 : length(background))
panel.polygon(background[[i]], col = names(background)[i],
border=NA)
}
#-- Display sample or row.names
for (i in 1 : nlevels(df$group))
{
if (display)
{
ltext(x = df$x[df$group == levels(df$group)[i]],
y = df$y[df$group == levels(df$group)[i]],
labels = groups[subscripts & df$group ==
levels(df$group)[i]], col = "white", cex = 0)
} else {
lpoints(x = df$x[df$group == levels(df$group)[i]],
y = df$y[df$group == levels(df$group)[i]],
col = "white", cex = 0, pch = 0)
}
}
#-- color samples according to col
for (i in unique(df$col))
{
if (display)
{
ltext(x = df$x[subscripts] [df$col[subscripts] == i],
y = df$y[subscripts] [df$col[subscripts] == i],
labels = groups[subscripts & df$col == i],
col = df[df$col == i, ]$col, cex =
df$cex[subscripts][df$col[subscripts] == i])
} else {
lpoints(x = df$x[subscripts] [df$col[subscripts] == i],
y = df$y[subscripts] [df$col[subscripts] == i],
col = df[df$col == i, ]$col,
cex = df$cex[subscripts][df$col[subscripts] == i],
pch = df$pch[subscripts][df$col[subscripts] == i])
}
}
}
)
print(p)
#the lattice plot needs to be printed in order to display the ellipse(s)
#-- centroid
if (centroid)
{
panels = trellis.currentLayout(which = "panel")
for (k in 1 : nlevels(df$Block))
{
other = df$Block %in% levels(df$Block)[k]
ind = which(panels == k, arr.ind = TRUE)
trellis.focus("panel", ind[2], ind[1], highlight = FALSE)
for (i in 1 : nlevels(df$group))
{
x0 = mean(df[other & df$group == levels(df$group)[i], ]$x)
y0 = mean(df[other & df$group == levels(df$group)[i], ]$y)
panel.points(x = x0, y = y0, col = unique(col.per.group)[i],
pch = 8, cex = df[other & df$group ==
levels(df$group)[i], ]$cex)
}
}
trellis.unfocus()
}
#-- star
if (star)
{
panels = trellis.currentLayout(which = "panel")
for (k in 1 : nlevels(df$Block))
{
other = df$Block %in% levels(df$Block)[k]
ind = which(panels == k, arr.ind = TRUE)
trellis.focus("panel", ind[2], ind[1], highlight = FALSE)
for (i in 1 : nlevels(df$group))
{
for (q in 1: length(df[other & df$group ==
levels(df$group)[i] , "x"]))
{
x0 = mean(df[other & df$group == levels(df$group)[i] ,
]$x)
y0 = mean(df[other & df$group == levels(df$group)[i] ,
]$y)
panel.segments(x0, y0, df[other & df$group ==
levels(df$group)[i], ]$x[q],
df[other & df$group == levels(df$group)[i], ]$y[q],
col = unique(col.per.group)[i], cex = df[other &
df$group == levels(df$group)[i], ]$cex,
pch = df[other & df$group == levels(df$group)[i], ]$pch)
}
}
}
trellis.unfocus()
}
#-- ellipse
if (ellipse)
{
panels = trellis.currentLayout(which = "panel")
for (k in 1 : nlevels(df$Block))
{
other.ellipse = df.ellipse$Block %in% levels(df$Block)[k]
ind = which(panels == k, arr.ind = TRUE)
trellis.focus("panel",ind[2], ind[1], highlight = FALSE)
for (i in 1 : nlevels(df$group))
{
panel.lines(x = df.ellipse[other.ellipse, paste0("Col",
2*(i - 1) + 1)],
y = df.ellipse[other.ellipse, paste0("Col", 2 * i)],
col = unique(col.per.group)[i])
}
}
trellis.unfocus()
}
}
#-- End: Lattice
if (style=="graphics")
{
#-- Start: graphics
#df$pch = as.numeric(df$pch) #number or names
opar = par(c("mai","mar","usr","cxy","xaxp","yaxp"))
reset.mfrow = FALSE
# if set to TRUE, the algorithm ends up with par(mfrow=reset.mfrow)
#-- Define layout
nResp = nlevels(df$Block)
if (is.null(layout))
{
# check if there are enough plots in mfrow
omfrow = par("mfrow")
available.plots = prod(omfrow)
if (available.plots<nResp)
# if not enough plots available, we create our new plot
{
nRows = min(c(3, ceiling(nResp/2)))
nCols = min(c(3, ceiling(nResp/nRows)))
layout = c(nRows, nCols)
par(mfrow = layout)
if (nRows * nCols < nResp)
devAskNewPage(TRUE)
reset.mfrow=TRUE # we changed mfrow to suits our needs,
#so we reset it at the end
}
} else {
if (length(layout) != 2 || !is.numeric(layout) ||
any(is.na(layout)))
stop("'layout' must be a numeric vector of length 2.")
nRows = layout[1]
nCols = layout[2]
par(mfrow = layout)
if (nRows * nCols < nResp)
devAskNewPage(TRUE)
}
for (k in 1 : nlevels(df$Block))
{
if (legend & group.pch == "same")
{
par(mai=c(1.360000, 1.093333, 1.093333,
(max(strwidth(c(levels(df$group),legend.title),"inches"))) + 1),
xpd=TRUE)
} else if(legend & group.pch == "different") {
par(mai=c(1.360000, 1.093333, 1.093333,
(max(strwidth(c(levels(df$group),legend.title,legend.title.pch),
"inches"))) + 1), xpd=TRUE)
}
other = df$Block %in% levels(df$Block)[k]
plot(df[other, "x" ], df[other, "y" ],
type = "n", xlab = X.label, ylab = Y.label,
xlim = c(xlim[[k]][1], xlim[[k]][2]), ylim = c(ylim[[k]][1],
ylim[[k]][2]),
cex.axis = size.axis, cex.lab = size.xlabel, lwd = point.lwd)#,...)
#-- initialise plot
if (nlevels(df$Block) == 1 & !any(class.object%in%c(object.mint,
"sgcca", "rgcca")))
# avoid double title when only one block is plotted
{
titlemain = NULL
if (ellipse)
other.ellipse = TRUE
}else{
titlemain = levels(df$Block)[k]
if (ellipse)
other.ellipse = df.ellipse$Block %in% levels(df$Block)[k]
}
#add title of the 'blocks'
title(main = titlemain, line = 1, cex.main = size.subtitle)
#-- Display sample or row.names
for (i in 1 : nlevels(df$group))
{
if (display.names)
{
text(x = df[df$group == levels(df$group)[i] & other, "x"],
y = df[df$group == levels(df$group)[i] & other, "y"],
labels = df[df$group == levels(df$group)[i] & other,
"names"],
col = "white", cex = 0,lwd=point.lwd)#,...)
} else {
points(x = df[df$group == levels(df$group)[i] & other, "x"],
y = df[df$group == levels(df$group)[i] & other, "y"],
col = "white", cex = 0, pch = 0,lwd=point.lwd)#,...)
}
}
#-- color samples according to col
for (i in unique(df$col))
{
if (display.names)
{
text(x = df[df$col == i & other, "x"],
y = df[df$col == i & other, "y"],
labels = df[df$col == i & other, "names"],
col = df[df$col == i, ]$col, cex = df[df$col == i, ]$cex,
lwd=point.lwd)#,...)
} else {
points(x = df[df$col == i & other, "x"],
y = df[df$col == i & other, "y"],
col = df[df$col == i, ]$col,
cex = df[df$col == i, ]$cex,
pch = as.numeric(df[df$col == i, ]$pch.levels),
lwd=point.lwd)#,...)
}
}
if (legend & group.pch == "same")
{
pch.legend = NULL
for (i in 1:nlevels(df$group))
pch.legend = c(pch.legend, df[df$group == levels(df$group)[i],
]$pch)
legend(par()$usr[2]+0.1, par()$usr[4] -
(par()$usr[4]-par()$usr[3])/2, col = col.per.group,
legend = levels(df$group), pch = if(display.names) {16} else
unique(df$pch.legend), title = legend.title, cex = size.legend,
lty = 0,lwd = point.lwd)
} else if(legend & group.pch == "different") {
legend(par()$usr[2]+0.1, par()$usr[4] -
(par()$usr[4]-par()$usr[3])/2,
col = c(NA, col.per.group, NA, NA, rep("black",
nlevels(df$pch.levels))),
legend = c(legend.title, levels(df$group), "",
legend.title.pch, levels(df$pch.levels)),
pch = c(NA, rep(16, length(col.per.group)), NA, NA, values.pch),
cex = max(c(size.legend.title, size.legend)),
lty = 0,
lwd = point.lwd
)
}
if (legend)
par(xpd=FALSE) # so the abline does not go outside the plot
#-- Abline
if (abline)
abline(v = 0, h = 0, lty = 2,lwd=point.lwd)#,...)
#-- Star
if (star == TRUE)
{
for (i in 1 : nlevels(df$group))
{
x0 = mean(df[df$group == levels(df$group)[i] & other, "x"])
y0 = mean(df[df$group == levels(df$group)[i] & other, "y"])
for (q in 1: length(df[df$group == levels(df$group)[i] &
other, "x"]))
{
segments(x0, y0, df[df$group == levels(df$group)[i] &
other, "x"][q], df[df$group == levels(df$group)[i] &
other, "y"][q],
cex = df$df[df$group == levels(df$group)[i] & other,
"cex"], col = df[df$group == levels(df$group)[i] &
other, "col"], lwd = point.lwd)#,...)
}
}
}
#-- Centroid
if (centroid == TRUE)
{
for (i in 1 : nlevels(df$group))
{
x0 = mean(df[df$group == levels(df$group)[i] & other, "x"])
y0 = mean(df[df$group == levels(df$group)[i] & other, "y"])
points(cbind(x0,y0), pch = 8, cex = df$df[df$group ==
levels(df$group)[i] & other, "cex"],
col = unique(col.per.group)[i], lwd = point.lwd)#,...)
}
}
#-- Ellipse
if (ellipse == TRUE)
{
for (i in 1 : nlevels(df$group))
{
lines(x = df.ellipse[other.ellipse,
paste0("Col", 2*(i - 1) + 1)],
y = df.ellipse[other.ellipse, paste0("Col", 2 * i)],
col = unique(col.per.group)[i],lwd=point.lwd)#,...)
}
}
#-- Background
if (!is.null(background)) # only first block: plsda and splsda
{
for (i in 1 : length(background))
polygon(background[[i]], col = names(background)[i], border=NA)
}
if (nlevels(df$Block) == 1 & !any(class.object%in%c(object.mint,
"sgcca", "rgcca")))
# avoid double title when only one block is plotted
{
title(title, line = 1, cex.main = size.title)#,...)
} else {
title(title, outer=TRUE, line = -2,cex.main = size.title)#,...)
}
}
#par(opar)
#par(usr=opar["usr"])
#par(xaxp=opar["xaxp"])
#par(yaxp=opar["yaxp"])
#par(mai=opar["mai"])
if (reset.mfrow)
par(mfrow = omfrow)
#par(mar=opar["mar"])
}
#-- End: graphics
if (style=="3d")
{
if(requireNamespace("rgl") == FALSE)
stop("the rgl package is required for 3d plots")
#-- Start: 3d
for (k in 1 : nlevels(df$Block))
{
rgl::open3d()
rgl::par3d(windowRect = c(500, 30, 1100, 630))
Sys.sleep(0.1)
if (!is.null(title))
{
mat = matrix(1:2, 2)
rgl::layout3d(mat, heights = c(1, 10), model = "inherit")
rgl::next3d()
rgl::text3d(0, 0, 0, title)
rgl::next3d()
}
if(any(class.object %in% c("ipca", "sipca", "pca", "spca", "prcomp",
"mixo_splsda", "mixo_plsda", "mixo_mlsplsda")))
{
other = TRUE
if (ellipse)
other.ellipse = TRUE
} else {
other = df$Block %in% levels(df$Block)[k]
if (ellipse)
other.ellipse = df.ellipse$Block %in% levels(df$Block)[k]
}
rgl::par3d(userMatrix = rgl::rotationMatrix(pi/80, 1, -1/(100*pi), 0))
if (legend)
{
rgl::legend3d(x = "right",
legend = levels(df$group),
col = col.per.group,
pch = rep(16,length(unique(df$pch))),
pt.cex = unique(df$cex),
bty = "n")
}
#-- Display sample or row.names
for (i in unique(df$col))
{
if (display.names)
{
for (cex_i in unique(df[df$col == i, ]$cex))
{
ind = which(df[df$col == i, ]$cex == cex_i)
rgl::text3d(x = df[df$col == i & other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i & other, "z"][ind],
texts = df[df$col == i & other, "names"][ind],
color = df[df$col == i, ]$col[ind], cex = cex_i)
}
}else{
cex = 20*df[df$col == i, ]$cex
for (pch_i in unique(df[df$col == i, ]$pch))
{
ind = which(df[df$col == i, ]$pch == pch_i)
if(pch_i == "sphere")
{
for (cex_i in unique(df[df$col == i, ]$cex[ind]))
{
ind_cex = which(df[df$col == i, ]$cex[ind] ==
cex_i)
rgl::points3d(x = df[df$col == i &
other, "x"][ind][ind_cex],
y = df[df$col == i & other, "y"][ind][ind_cex],
z = df[df$col == i & other, "z"][ind][ind_cex],
col = df[df$col == i, ]$col[ind][ind_cex],
size = cex_i*20, radius = cex_i, add = TRUE)
}
} else if (pch_i == "tetra") {
rgl::shapelist3d(rgl::tetrahedron3d(), x = df[df$col == i &
other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i & other, "z"][ind],
col = df[df$col == i, ]$col[ind], size =
cex[ind]/25)
} else if (pch_i == "cube") {
rgl::shapelist3d(rgl::cube3d(),x = df[df$col == i &
other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i & other, "z"][ind],
col = df[df$col == i, ]$col[ind], size =
cex[ind]/30)
} else if (pch_i == "octa") {
rgl::shapelist3d(rgl::octahedron3d(), x = df[df$col == i &
other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i & other, "z"][ind],
col = df[df$col == i, ]$col[ind], size =
cex[ind]/17)
} else if (pch_i == "icosa") {
rgl::shapelist3d(rgl::icosahedron3d(), x = df[df$col == i &
other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i &other, "z"][ind],
col = df[df$col == i, ]$col[ind], size =
cex[ind]/20)
} else if (pch_i == "dodeca") {
rgl::shapelist3d(rgl::dodecahedron3d(), x = df[df$col == i &
other, "x"][ind],
y = df[df$col == i & other, "y"][ind],
z = df[df$col == i & other, "z"][ind],
col = df[df$col == i, ]$col[ind], size =
cex[ind]/20)
}
}
}
}
#-- Ellipse
if (ellipse)
{
coords = matrix(cbind(df[other, "x"],
df[other, "y"],
df[other,"z"]),ncol = 3)
centr.coords = apply(coords, 2, function(x)
tapply(x, df$group, mean))
if (length(unique(df$group)) == 1)
centr.coords = matrix(centr.coords, nrow=1)
rownames(centr.coords) = levels(df$group)
lg = levels(df$group)
for(i in 1:length(lg))
{
g = lg[i]
sel = df$group == g
s = cov(coords[sel, , drop = FALSE])
cc = centr.coords[i,]
# lines(ellipse(s, centre=cc), col=unique(col.per.group)[i])
rgl::shade3d(rgl::ellipse3d(s, centre = cc, level =
df.ellipse$ellipse.level[1]), col=unique(col.per.group)[i],
alpha = alpha)
}
}
#-- Centroid
if (centroid == TRUE)
{
for (i in 1 : nlevels(df$group))
{
x0 = mean(df[df$group == levels(df$group)[i] & other, "x"])
y0 = mean(df[df$group == levels(df$group)[i] & other, "y"])
z0 = mean(df[df$group == levels(df$group)[i] & other, "z"])
rgl::points3d(x=x0, y=y0,z=z0, cex=df$df[df$group ==
levels(df$group)[i] & other, "cex"], col =
unique(col.per.group)[i])
}
}
#-- Star
if (star == TRUE)
{
for (i in 1 : nlevels(df$group))
{
x0 = mean(df[df$group == levels(df$group)[i] & other, "x"])
y0 = mean(df[df$group == levels(df$group)[i] & other, "y"])
z0 = mean(df[df$group == levels(df$group)[i] & other, "z"])
for (q in 1: length(df[df$group == levels(df$group)[i] &
other, "x"]))
{
rgl::segments3d(x=c(x0, df[df$group == levels(df$group)[i] &
other, "x"][q]), y=c(y0,df[df$group ==
levels(df$group)[i] & other, "y"][q]),
z=c(z0, df[df$group == levels(df$group)[i] &
other, "z"][q]),
cex=df$df[df$group == levels(df$group)[i] &
other, "cex"], col=df[df$group == levels(df$group)[i] &
other, "col"])
}
}
}
#-- draws axes/box --#
if (axes.box == "box")
{
rgl::axes3d(marklen = 25)
rgl::box3d()
}
if (axes.box == "bbox")
{
rgl::bbox3d(color = c("#333377", "black"), emission = gray(0.5),
specular = gray(0.1), shininess = 5, alpha = 0.8, marklen = 25)
}
if (axes.box == "both")
{
rgl::axes3d(marklen = 25); rgl::box3d()
rgl::bbox3d(color = c("#333377", "black"), emission = gray(0.5),
specular = gray(0.1), shininess = 5, alpha = 0.8, marklen = 25)
}
#-- add axes labels --#
rgl::mtext3d(X.label, "x-+", line = 1)
rgl::mtext3d(Y.label, "y-+", line = 1.5)
rgl::mtext3d(Z.label, "z+-", line = 1)
if (! any(class.object%in% c("ipca", "sipca", "pca", "spca",
"prcomp", "mixo_splsda", "mixo_plsda", "mixo_mlsplsda")))
rgl::title3d(main = levels(df$Block)[k])
}
#-- output --#
return(invisible(cbind(df$x, df$y, df$z)))
}
if (style%in%c("graphics","3d"))
p = NULL
return(p)
}
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