R/cnvGSAviz.R
In JoeLugo/cnvGSA: Gene Set Analysis of (Rare) Copy Number Variants
# VIZ
#' Creates the plots from the CnvGSAOutput data.
#'
#' @param cnvGSA.in A CnvGSAInput S4 object.
#' @param cnvGSA.out A CnvGSAOutput S4 object.
#' @return Creates the plots to better understand the output.
#' @examples
#' ## See vignette for full details and worked example
# f.makeViz(cnvGSA.in,cnvGSA.out)
f.makeViz <- function(cnvGSA.in,cnvGSA.out)
{
t <- Sys.time()
timestamp <- strftime(t,"%Y%m%d%Hh%Mm%S")
vizData <- list(cnvGSA.in@gsData.ls$gs_all.ls,cnvGSA.out@res.ls,cnvGSA.in@cnvData.ls$cnv.df,cnvGSA.in@phData.ls$ph_TYPE.df)
names(vizData) <- list("gs_all.ls","res.ls","cnv.df","ph_TYPE.df")
setwd (cnvGSA.in@config.ls$outputPath)
save(vizData,file=paste("vizInput_",timestamp,".RData",sep=""))
config.df <- cnvGSA.in@config.ls$config.df
Kl <- config.df[config.df$param == "Kl","value"]
gsList <- config.df[config.df$param == "gsList","value"]
cnvType <- config.df[config.df$param == "cnvType","value"]
outputPathViz <- config.df[config.df$param == "outputPathViz","value"]
labelSize <- as.numeric(config.df[config.df$param == "labelSize","value"])
plotHeight <- as.numeric(config.df[config.df$param == "plotHeight","value"])
FDRThreshold <- as.numeric(config.df[config.df$param == "FDRThreshold","value"])
correctionViz <- gsub(" ","",unlist(strsplit(config.df[config.df$param == "correctionViz","value"],",")),fixed=TRUE)
if (Kl == "") {Kl <- "ALL"}
if (is.na(FDRThreshold)) {FDRThreshold <- 0.1}
if (is.na(plotHeight)) {plotHeight <- 13}
if (is.na(labelSize)) {labelSize <- 0.7}
if(length(correctionViz) == 0) {correctionViz <- gsub(" ","",unlist(strsplit(config.df[config.df$param == "corrections","value"],",")),fixed=TRUE)} # just assign value from general parameters GP20171012
res.ls <- vizData$res.ls
if ( Kl == "YES") { gsID.chv <- get(paste("covAll_chipAll_",cnvType,"_KLy.df",sep=""),res.ls)$GsID }
if ( Kl == "NO") { gsID.chv <- get(paste("covAll_chipAll_",cnvType,"_KLn.df",sep=""),res.ls)$GsID }
if ( Kl == "ALL") { gsID.chv <- get(paste("covAll_chipAll_",cnvType,"_KLy.df",sep=""),res.ls)$GsID }
if (gsList != ""){
gsList <- gsub(" ","",unlist(strsplit(readLines(gsList),",")),fixed=TRUE)
gsList <- gsList[gsList %in% gsID.chv]
cat("Only using gene-sets that are in the $res.ls data frames.")
cat("\n")
}
else{
stop("No genes to plot. Check the gene-set list you are using.")
}
if (length(gsList) == 0){
stop("No valid genes to plot. Please check that gene-sets are in the $res.ls data frames.")
}
gs_all.ls <- vizData$gs_all.ls
cnv.df <- vizData$cnv.df
if (length(gsList) == 0){
stop("No gene-sets in gsList.")
}
gs_len.nv <- sapply (gs_all.ls, length)
setwd (outputPathViz)
cat(paste("Changing directory to ",outputPathViz,sep=""))
cat("\n")
# 1.
# NEUROFUNCTION + SYNAPTIC
z_set.gsid <- gsList
z_olp.n <- length (z_set.gsid)
z_olp.mx <- matrix (data = NA, ncol = z_olp.n, nrow = z_olp.n, dimnames = list (z_set.gsid, z_set.gsid))
# finding how many common gsList there are between the gene sets
for (i in 1: z_olp.n)
{
for (j in 1: z_olp.n)
{
zi.gid <- gs_all.ls[[z_set.gsid[i]]]; zj.gid <- gs_all.ls[[z_set.gsid[j]]]
z_olp.mx[i, j] <- length (intersect (zi.gid, zj.gid)) / length (zi.gid) * 100
}
}
rm (i, j)
z_olp.df <- as.data.frame(z_olp.mx)
z_olp.df <- cbind(GeneSets = row.names(z_olp.df),z_olp.df)
row.names(z_olp.df) <- NULL
write.table (z_olp.df, col.names = T, row.names = F, sep = "\t", quote = F, file = paste("GsOverlap_",timestamp,".txt",sep=""))
# cnvType: NEUROFUNCTION + SYNAPTIC
z_set.gsid <- gsList
z_set.labels <- paste (z_set.gsid, gs_len.nv[z_set.gsid], sep = ": ")
if (Kl == "ALL"){
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set2.col <- rep ("gray30", length (z_set.gsid))
z_set1_U.col <- rep ("gray30", length (z_set.gsid))
z_set2_U.col <- rep ("gray30", length (z_set.gsid))
z_set1_TL.col <- rep ("gray30", length (z_set.gsid))
z_set2_TL.col <- rep ("gray30", length (z_set.gsid))
z_set1_CNML.col <- rep ("gray30", length (z_set.gsid))
z_set2_CNML.col <- rep ("gray30", length (z_set.gsid))
resObjectKly <- get(paste("covAll_chipAll_",cnvType,"_KLy.df",sep=""),res.ls)
resObjectKln <- get(paste("covAll_chipAll_",cnvType,"_KLn.df",sep=""),res.ls)
z_set1.df <- resObjectKly[match (z_set.gsid, resObjectKly$GsID), ]
z_set2.df <- resObjectKln[match (z_set.gsid, resObjectKln$GsID), ]
height_U.mx <- matrix (data = c (z_set1.df$Pvalue_U_dev_s, z_set2.df$Pvalue_U_dev_s), nrow = 2, byrow = T)
height_c.mx <- matrix (data = c (z_set1.df$Coeff, z_set2.df$Coeff), nrow = 2, byrow = T)
height_Uc.mx <- matrix (data = c (z_set1.df$Coeff_U, z_set2.df$Coeff_U), nrow = 2, byrow = T)
height_TLc.mx <- matrix (data = c (z_set1.df$Coeff_TL, z_set2.df$Coeff_TL), nrow = 2, byrow = T)
height_CNMLc.mx <- matrix (data = c (z_set1.df$Coeff_CNML, z_set2.df$Coeff_CNML), nrow = 2, byrow = T)
z_set1.col[which (z_set1.df$FDR_BH <= FDRThreshold)] <- "brown"
z_set2.col[which (z_set2.df$FDR_BH <= FDRThreshold)] <- "brown"
z_set1_U.col[which (z_set1.df$FDR_BH_U <= FDRThreshold)] <- "brown"
z_set2_U.col[which (z_set2.df$FDR_BH_U <= FDRThreshold)] <- "brown"
z_set1_TL.col[which (z_set1.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
z_set2_TL.col[which (z_set2.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
z_set1_CNML.col[which (z_set1.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
z_set2_CNML.col[which (z_set2.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border.vc <- c (z_set1.col, z_set2.col)
border_U.vc <- c (z_set1_U.col, z_set2_U.col)
border_TL.vc <- c (z_set1_TL.col, z_set2_TL.col)
border_CNML.vc <- c (z_set1_CNML.col, z_set2_CNML.col)
nc.vc <- z_set1.col
nc_U.vc <- z_set1_U.col
nc_TL.vc <- z_set1_TL.col
nc_CNML.vc <- z_set1_CNML.col
} else if (Kl == "YES"){
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set1_U.col <- rep ("gray30", length (z_set.gsid))
z_set1_TL.col <- rep ("gray30", length (z_set.gsid))
z_set1_CNML.col <- rep ("gray30", length (z_set.gsid))
resObjectKly <- get(paste("covAll_chipAll_",cnvType,"_KLy.df",sep=""),res.ls)
z_set1.df <- resObjectKly[match (z_set.gsid, resObjectKly$GsID), ]
height_U.mx <- matrix (data = c (z_set1.df$Pvalue_U_dev_s), nrow = 1, byrow = T)
height_c.mx <- matrix (data = c (z_set1.df$Coeff), nrow = 1, byrow = T)
height_Uc.mx <- matrix (data = c (z_set1.df$Coeff_U), nrow = 1, byrow = T)
height_TLc.mx <- matrix (data = c (z_set1.df$Coeff_TL), nrow = 1, byrow = T)
height_CNMLc.mx <- matrix (data = c (z_set1.df$Coeff_CNML), nrow = 1, byrow = T)
z_set1.col[which (z_set1.df$FDR_BH <= FDRThreshold)] <- "brown"
border.vc <- c (z_set1.col)
z_set1_U.col[which (z_set1.df$FDR_BH_U <= FDRThreshold)] <- "brown"
border_U.vc <- c (z_set1_U.col)
z_set1_TL.col[which (z_set1.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
border_TL.vc <- c (z_set1_TL.col)
z_set1_CNML.col[which (z_set1.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border_CNML.vc <- c (z_set1_CNML.col)
nc.vc <- z_set1.col
nc_U.vc <- z_set1_U.col
nc_TL.vc <- z_set1_TL.col
nc_CNML.vc <- z_set1_CNML.col
} else if (Kl == "NO"){
z_set2.col <- rep ("gray30", length (z_set.gsid))
z_set2_U.col <- rep ("gray30", length (z_set.gsid))
z_set2_TL.col <- rep ("gray30", length (z_set.gsid))
z_set2_CNML.col <- rep ("gray30", length (z_set.gsid))
resObjectKln <- get(paste("covAll_chipAll_",cnvType,"_KLn.df",sep=""),res.ls)
z_set2.df <- resObjectKln[match (z_set.gsid, resObjectKln$GsID), ]
height_U.mx <- matrix (data = c (z_set2.df$Pvalue_U_dev_s), nrow = 1, byrow = T)
height_c.mx <- matrix (data = c (z_set2.df$Coeff), nrow = 1, byrow = T)
height_Uc.mx <- matrix (data = c (z_set2.df$Coeff_U), nrow = 1, byrow = T)
height_TLc.mx <- matrix (data = c (z_set2.df$Coeff_TL), nrow = 1, byrow = T)
height_CNMLc.mx <- matrix (data = c (z_set2.df$Coeff_CNML), nrow = 1, byrow = T)
z_set2.col[which (z_set2.df$FDR_BH <= FDRThreshold)] <- "brown"
border.vc <- c (z_set2.col)
z_set2_U.col[which (z_set2.df$FDR_BH_U <= FDRThreshold)] <- "brown"
border_U.vc <- c (z_set2_U.col)
z_set2_TL.col[which (z_set2.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
border_TL.vc <- c (z_set2_TL.col)
z_set2_CNML.col[which (z_set2.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border_CNML.vc <- c (z_set2_CNML.col)
nc.vc <- z_set2.col
nc_U.vc <- z_set2_U.col
nc_TL.vc <- z_set2_TL.col
nc_CNML.vc <- z_set2_CNML.col
}
# if ("no_corr" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){#GP20171012
if ("no_corr" %in% correctionViz || "ALL" %in% correctionViz){
rangeVals <- range(height_c.mx, na.rm=TRUE,finite=TRUE)
rangeVals[1] <- min(0,rangeVals[1])
rangeVals[2] <- ceiling(rangeVals[2])
pdf(paste(cnvType,"_EffectSize_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Effect Size",sep=""),
height = height_c.mx,
names.arg = z_set.labels, ylim = rangeVals, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border.vc, ncol = length (nc.vc), byrow = T)),
ylab = "Coeff")
dev.off()
}
# if ("uni_gc" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){#GP20171012
if ("uni_gc" %in% correctionViz || "ALL" %in% correctionViz){
rangeVals_U <- range(height_Uc.mx, na.rm=TRUE,finite=TRUE)
rangeVals_U[1] <- min(0,rangeVals_U[1])
rangeVals_U[2] <- ceiling(rangeVals_U[2])
pdf(paste(cnvType,"_EffectSize_U_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Effect Size: U",sep=""),
height = height_Uc.mx,
names.arg = z_set.labels, ylim = rangeVals_U, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_U.vc, ncol = length (nc_U.vc), byrow = T)),
ylab = "Coeff_U")
dev.off()
}
# if ("tot_l" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){#GP20171012
if ("tot_l" %in% correctionViz || "ALL" %in% correctionViz) {
rangeVals_TL <- range(height_TLc.mx, na.rm=TRUE,finite=TRUE)
rangeVals_TL[1] <- min(0,rangeVals_TL[1])
rangeVals_TL[2] <- ceiling(rangeVals_TL[2])
pdf(paste(cnvType,"_EffectSize_TL_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Effect Size: TL",sep=""),
height = height_TLc.mx,
names.arg = z_set.labels, ylim = rangeVals_TL, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_TL.vc, ncol = length (nc_TL.vc), byrow = T)),
ylab = "Coeff_TL")
dev.off()
}
# if ("cnvn_ml" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){#GP20171012
if ("cnvn_ml" %in% correctionViz || "ALL" %in% correctionViz){
rangeVals_CNML <- range(height_CNMLc.mx, na.rm=TRUE,finite=TRUE)
rangeVals_CNML[1] <- min(0,rangeVals_CNML[1])
rangeVals_CNML[2] <- ceiling(rangeVals_CNML[2])
pdf(paste(cnvType,"_EffectSize_CNML_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Effect Size: CNML",sep=""),
height = height_CNMLc.mx,
names.arg = z_set.labels, ylim = rangeVals_CNML, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_CNML.vc, ncol = length (nc_CNML.vc), byrow = T)),
ylab = "Coeff_CNML")
dev.off()
}
z_set.gsid <- gsList
z_set.labels <- paste (z_set.gsid, gs_len.nv[z_set.gsid], sep = ": ")
z_col.names <- c ("CASE_g1n", "CTRL_g1n", "CASE_g2n", "CTRL_g2n", "CASE_g3n", "CTRL_g3n")
pdf(paste(cnvType,"_Support_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 1)
if (Kl == "ALL"){
height_s.mx <- rbind (t (z_set1.df[, z_col.names]), t (z_set2.df[, z_col.names]))
} else if (Kl == "YES"){
height_s.mx <- t (z_set1.df[, z_col.names])
} else if (Kl == "NO"){
height_s.mx <- t (z_set2.df[, z_col.names])
}
rangeVals_s <- range(height_s.mx, na.rm=TRUE,finite=TRUE)
rangeVals_s[1] <- min(0,rangeVals_s[1])
rangeVals_s[2] <- ceiling(rangeVals_s[2])
barplot (
main = paste(cnvType,": Support",sep=""),
height = height_s.mx,
names.arg = z_set.labels, ylim = rangeVals_s, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("salmon", "skyblue"), times = length (z_set.labels)),
border = "gray30",
ylab = "CASE and CTRL subject %")
dev.off()
z_set.gsid <- gsList
z_set.labels <- paste (z_set.gsid, gs_len.nv[z_set.gsid], sep = ": ")
if (Kl == "ALL"){
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set2.col <- rep ("gray30", length (z_set.gsid))
z_set1_U.col <- rep ("gray30", length (z_set.gsid))
z_set2_U.col <- rep ("gray30", length (z_set.gsid))
z_set1_TL.col <- rep ("gray30", length (z_set.gsid))
z_set2_TL.col <- rep ("gray30", length (z_set.gsid))
z_set1_CNML.col <- rep ("gray30", length (z_set.gsid))
z_set2_CNML.col <- rep ("gray30", length (z_set.gsid))
height.mx <- matrix (data = c (z_set1.df$Pvalue_dev_s, z_set2.df$Pvalue_dev_s), nrow = 2, byrow = T)
height_U.mx <- matrix (data = c (z_set1.df$Pvalue_U_dev_s, z_set2.df$Pvalue_U_dev_s), nrow = 2, byrow = T)
height_TL.mx <- matrix (data = c (z_set1.df$Pvalue_TL_dev_s, z_set2.df$Pvalue_TL_dev_s), nrow = 2, byrow = T)
height_CNML.mx <- matrix (data = c (z_set1.df$Pvalue_CNML_dev_s, z_set2.df$Pvalue_CNML_dev_s), nrow = 2, byrow = T)
z_set1.col[which (z_set1.df$FDR_BH <= FDRThreshold)] <- "brown"
z_set2.col[which (z_set2.df$FDR_BH <= FDRThreshold)] <- "brown"
z_set1_U.col[which (z_set1.df$FDR_BH_U <= FDRThreshold)] <- "brown"
z_set2_U.col[which (z_set2.df$FDR_BH_U <= FDRThreshold)] <- "brown"
z_set1_TL.col[which (z_set1.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
z_set2_TL.col[which (z_set2.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
z_set1_CNML.col[which (z_set1.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
z_set2_CNML.col[which (z_set2.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border.vc <- c (z_set1.col, z_set2.col)
border_U.vc <- c (z_set1_U.col, z_set2_U.col)
border_TL.vc <- c (z_set1_TL.col, z_set2_TL.col)
border_CNML.vc <- c (z_set1_CNML.col, z_set2_CNML.col)
nc.vc <- z_set1.col
nc_U.vc <- z_set1_U.col
nc_TL.vc <- z_set1_TL.col
nc_CNML.vc <- z_set1_CNML.col
} else if (Kl == "YES"){
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set1_U.col <- rep ("gray30", length (z_set.gsid))
z_set1_TL.col <- rep ("gray30", length (z_set.gsid))
z_set1_CNML.col <- rep ("gray30", length (z_set.gsid))
height.mx <- matrix (data = c (z_set1.df$Pvalue_dev_s), nrow = 1, byrow = T)
height_U.mx <- matrix (data = c (z_set1.df$Pvalue_U_dev_s), nrow = 1, byrow = T)
height_TL.mx <- matrix (data = c (z_set1.df$Pvalue_TL_dev_s), nrow = 1, byrow = T)
height_CNML.mx <- matrix (data = c (z_set1.df$Pvalue_CNML_dev_s), nrow = 1, byrow = T)
z_set1.col[which (z_set1.df$FDR_BH <= FDRThreshold)] <- "brown"
border.vc <- c (z_set1.col)
z_set1_U.col[which (z_set1.df$FDR_BH_U <= FDRThreshold)] <- "brown"
border_U.vc <- c (z_set1_U.col)
z_set1_TL.col[which (z_set1.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
border_TL.vc <- c (z_set1_TL.col)
z_set1_CNML.col[which (z_set1.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border_CNML.vc <- c (z_set1_CNML.col)
nc.vc <- z_set1.col
nc_U.vc <- z_set1_U.col
nc_TL.vc <- z_set1_TL.col
nc_CNML.vc <- z_set1_CNML.col
} else if (Kl == "NO"){
z_set2.col <- rep ("gray30", length (z_set.gsid))
z_set2_U.col <- rep ("gray30", length (z_set.gsid))
z_set2_TL.col <- rep ("gray30", length (z_set.gsid))
z_set2_CNML.col <- rep ("gray30", length (z_set.gsid))
height.mx <- matrix (data = c (z_set2.df$Pvalue_dev_s), nrow = 1, byrow = T)
height_U.mx <- matrix (data = c (z_set2.df$Pvalue_U_dev_s), nrow = 1, byrow = T)
height_TL.mx <- matrix (data = c (z_set2.df$Pvalue_TL_dev_s), nrow = 1, byrow = T)
height_CNML.mx <- matrix (data = c (z_set2.df$Pvalue_CNML_dev_s), nrow = 1, byrow = T)
z_set2.col[which (z_set2.df$FDR_BH <= FDRThreshold)] <- "brown"
border.vc <- c (z_set2.col)
z_set2_U.col[which (z_set2.df$FDR_BH_U <= FDRThreshold)] <- "brown"
border_U.vc <- c (z_set2_U.col)
z_set2_TL.col[which (z_set2.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
border_TL.vc <- c (z_set2_TL.col)
z_set2_CNML.col[which (z_set2.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border_CNML.vc <- c (z_set2_CNML.col)
nc.vc <- z_set2.col
nc_U.vc <- z_set2_U.col
nc_TL.vc <- z_set2_TL.col
nc_CNML.vc <- z_set2_CNML.col
}
min.n <- min (c (min (height_U.mx), min (height_TL.mx), min (height_CNML.mx)))
max.n <- max (c (max (height_U.mx), max (height_TL.mx), max (height_CNML.mx)))
if ("no_corr" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){
rangeVals <- range(height.mx, na.rm=TRUE,finite=TRUE)
rangeVals[1] <- min(0,rangeVals[1])
rangeVals[2] <- ceiling(rangeVals[2])
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set2.col <- rep ("gray30", length (z_set.gsid))
pdf(paste(cnvType,"_Significance_Compare_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Compare Significance:",sep=""),
height = height.mx,
names.arg = z_set.labels, ylim = rangeVals, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border.vc, ncol = length (nc.vc), byrow = T)),
ylab = "-Log (Dev P-value) * sign (Coeff)")
dev.off()
}
if ("uni_gc" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){
rangeVals_U <- range(height_U.mx, na.rm=TRUE,finite=TRUE)
rangeVals_U[1] <- min(0,rangeVals_U[1])
rangeVals_U[2] <- ceiling(rangeVals_U[2])
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set2.col <- rep ("gray30", length (z_set.gsid))
pdf(paste(cnvType,"_Significance_Compare_U_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Compare Significance: U",sep=""),
height = height_U.mx,
names.arg = z_set.labels, ylim = rangeVals_U, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_U.vc, ncol = length (nc_U.vc), byrow = T)),
ylab = "-Log (Dev P-value) * sign (Coeff)")
dev.off()
}
if ("tot_l" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){
rangeVals_TL <- range(height_TL.mx, na.rm=TRUE,finite=TRUE)
rangeVals_TL[1] <- min(0,rangeVals_TL[1])
rangeVals_TL[2] <- ceiling(rangeVals_TL[2])
pdf(paste(cnvType,"_Significance_Compare_TL_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Compare Significance: TL",sep=""),
height = height_TL.mx,
names.arg = z_set.labels, ylim = rangeVals_TL, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_TL.vc, ncol = length (nc_TL.vc), byrow = T)),
ylab = "-Log (Dev P-value) * sign (Coeff)")
dev.off()
}
if ("cnvn_ml" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){
rangeVals_CNML <- range(height_CNML.mx, na.rm=TRUE,finite=TRUE)
rangeVals_CNML[1] <- min(0,rangeVals_CNML[1])
rangeVals_CNML[2] <- ceiling(rangeVals_CNML[2])
pdf(paste(cnvType,"_Significance_Compare_CNML_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Compare Significance: CNML",sep=""),
height = height_CNML.mx,
names.arg = z_set.labels, ylim = rangeVals_CNML, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_CNML.vc, ncol = length (nc_CNML.vc), byrow = T)),
ylab = "-Log (Dev P-value) * sign (Coeff)")
dev.off()
}
}
JoeLugo/cnvGSA documentation built on May 28, 2019, 12:55 p.m.
R Package Documentation
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# VIZ
#' Creates the plots from the CnvGSAOutput data.
#'
#' @param cnvGSA.in A CnvGSAInput S4 object.
#' @param cnvGSA.out A CnvGSAOutput S4 object.
#' @return Creates the plots to better understand the output.
#' @examples
#' ## See vignette for full details and worked example
# f.makeViz(cnvGSA.in,cnvGSA.out)
f.makeViz <- function(cnvGSA.in,cnvGSA.out)
{
t <- Sys.time()
timestamp <- strftime(t,"%Y%m%d%Hh%Mm%S")
vizData <- list(cnvGSA.in@gsData.ls$gs_all.ls,cnvGSA.out@res.ls,cnvGSA.in@cnvData.ls$cnv.df,cnvGSA.in@phData.ls$ph_TYPE.df)
names(vizData) <- list("gs_all.ls","res.ls","cnv.df","ph_TYPE.df")
setwd (cnvGSA.in@config.ls$outputPath)
save(vizData,file=paste("vizInput_",timestamp,".RData",sep=""))
config.df <- cnvGSA.in@config.ls$config.df
Kl <- config.df[config.df$param == "Kl","value"]
gsList <- config.df[config.df$param == "gsList","value"]
cnvType <- config.df[config.df$param == "cnvType","value"]
outputPathViz <- config.df[config.df$param == "outputPathViz","value"]
labelSize <- as.numeric(config.df[config.df$param == "labelSize","value"])
plotHeight <- as.numeric(config.df[config.df$param == "plotHeight","value"])
FDRThreshold <- as.numeric(config.df[config.df$param == "FDRThreshold","value"])
correctionViz <- gsub(" ","",unlist(strsplit(config.df[config.df$param == "correctionViz","value"],",")),fixed=TRUE)
if (Kl == "") {Kl <- "ALL"}
if (is.na(FDRThreshold)) {FDRThreshold <- 0.1}
if (is.na(plotHeight)) {plotHeight <- 13}
if (is.na(labelSize)) {labelSize <- 0.7}
if(length(correctionViz) == 0) {correctionViz <- gsub(" ","",unlist(strsplit(config.df[config.df$param == "corrections","value"],",")),fixed=TRUE)} # just assign value from general parameters GP20171012
res.ls <- vizData$res.ls
if ( Kl == "YES") { gsID.chv <- get(paste("covAll_chipAll_",cnvType,"_KLy.df",sep=""),res.ls)$GsID }
if ( Kl == "NO") { gsID.chv <- get(paste("covAll_chipAll_",cnvType,"_KLn.df",sep=""),res.ls)$GsID }
if ( Kl == "ALL") { gsID.chv <- get(paste("covAll_chipAll_",cnvType,"_KLy.df",sep=""),res.ls)$GsID }
if (gsList != ""){
gsList <- gsub(" ","",unlist(strsplit(readLines(gsList),",")),fixed=TRUE)
gsList <- gsList[gsList %in% gsID.chv]
cat("Only using gene-sets that are in the $res.ls data frames.")
cat("\n")
}
else{
stop("No genes to plot. Check the gene-set list you are using.")
}
if (length(gsList) == 0){
stop("No valid genes to plot. Please check that gene-sets are in the $res.ls data frames.")
}
gs_all.ls <- vizData$gs_all.ls
cnv.df <- vizData$cnv.df
if (length(gsList) == 0){
stop("No gene-sets in gsList.")
}
gs_len.nv <- sapply (gs_all.ls, length)
setwd (outputPathViz)
cat(paste("Changing directory to ",outputPathViz,sep=""))
cat("\n")
# 1.
# NEUROFUNCTION + SYNAPTIC
z_set.gsid <- gsList
z_olp.n <- length (z_set.gsid)
z_olp.mx <- matrix (data = NA, ncol = z_olp.n, nrow = z_olp.n, dimnames = list (z_set.gsid, z_set.gsid))
# finding how many common gsList there are between the gene sets
for (i in 1: z_olp.n)
{
for (j in 1: z_olp.n)
{
zi.gid <- gs_all.ls[[z_set.gsid[i]]]; zj.gid <- gs_all.ls[[z_set.gsid[j]]]
z_olp.mx[i, j] <- length (intersect (zi.gid, zj.gid)) / length (zi.gid) * 100
}
}
rm (i, j)
z_olp.df <- as.data.frame(z_olp.mx)
z_olp.df <- cbind(GeneSets = row.names(z_olp.df),z_olp.df)
row.names(z_olp.df) <- NULL
write.table (z_olp.df, col.names = T, row.names = F, sep = "\t", quote = F, file = paste("GsOverlap_",timestamp,".txt",sep=""))
# cnvType: NEUROFUNCTION + SYNAPTIC
z_set.gsid <- gsList
z_set.labels <- paste (z_set.gsid, gs_len.nv[z_set.gsid], sep = ": ")
if (Kl == "ALL"){
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set2.col <- rep ("gray30", length (z_set.gsid))
z_set1_U.col <- rep ("gray30", length (z_set.gsid))
z_set2_U.col <- rep ("gray30", length (z_set.gsid))
z_set1_TL.col <- rep ("gray30", length (z_set.gsid))
z_set2_TL.col <- rep ("gray30", length (z_set.gsid))
z_set1_CNML.col <- rep ("gray30", length (z_set.gsid))
z_set2_CNML.col <- rep ("gray30", length (z_set.gsid))
resObjectKly <- get(paste("covAll_chipAll_",cnvType,"_KLy.df",sep=""),res.ls)
resObjectKln <- get(paste("covAll_chipAll_",cnvType,"_KLn.df",sep=""),res.ls)
z_set1.df <- resObjectKly[match (z_set.gsid, resObjectKly$GsID), ]
z_set2.df <- resObjectKln[match (z_set.gsid, resObjectKln$GsID), ]
height_U.mx <- matrix (data = c (z_set1.df$Pvalue_U_dev_s, z_set2.df$Pvalue_U_dev_s), nrow = 2, byrow = T)
height_c.mx <- matrix (data = c (z_set1.df$Coeff, z_set2.df$Coeff), nrow = 2, byrow = T)
height_Uc.mx <- matrix (data = c (z_set1.df$Coeff_U, z_set2.df$Coeff_U), nrow = 2, byrow = T)
height_TLc.mx <- matrix (data = c (z_set1.df$Coeff_TL, z_set2.df$Coeff_TL), nrow = 2, byrow = T)
height_CNMLc.mx <- matrix (data = c (z_set1.df$Coeff_CNML, z_set2.df$Coeff_CNML), nrow = 2, byrow = T)
z_set1.col[which (z_set1.df$FDR_BH <= FDRThreshold)] <- "brown"
z_set2.col[which (z_set2.df$FDR_BH <= FDRThreshold)] <- "brown"
z_set1_U.col[which (z_set1.df$FDR_BH_U <= FDRThreshold)] <- "brown"
z_set2_U.col[which (z_set2.df$FDR_BH_U <= FDRThreshold)] <- "brown"
z_set1_TL.col[which (z_set1.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
z_set2_TL.col[which (z_set2.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
z_set1_CNML.col[which (z_set1.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
z_set2_CNML.col[which (z_set2.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border.vc <- c (z_set1.col, z_set2.col)
border_U.vc <- c (z_set1_U.col, z_set2_U.col)
border_TL.vc <- c (z_set1_TL.col, z_set2_TL.col)
border_CNML.vc <- c (z_set1_CNML.col, z_set2_CNML.col)
nc.vc <- z_set1.col
nc_U.vc <- z_set1_U.col
nc_TL.vc <- z_set1_TL.col
nc_CNML.vc <- z_set1_CNML.col
} else if (Kl == "YES"){
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set1_U.col <- rep ("gray30", length (z_set.gsid))
z_set1_TL.col <- rep ("gray30", length (z_set.gsid))
z_set1_CNML.col <- rep ("gray30", length (z_set.gsid))
resObjectKly <- get(paste("covAll_chipAll_",cnvType,"_KLy.df",sep=""),res.ls)
z_set1.df <- resObjectKly[match (z_set.gsid, resObjectKly$GsID), ]
height_U.mx <- matrix (data = c (z_set1.df$Pvalue_U_dev_s), nrow = 1, byrow = T)
height_c.mx <- matrix (data = c (z_set1.df$Coeff), nrow = 1, byrow = T)
height_Uc.mx <- matrix (data = c (z_set1.df$Coeff_U), nrow = 1, byrow = T)
height_TLc.mx <- matrix (data = c (z_set1.df$Coeff_TL), nrow = 1, byrow = T)
height_CNMLc.mx <- matrix (data = c (z_set1.df$Coeff_CNML), nrow = 1, byrow = T)
z_set1.col[which (z_set1.df$FDR_BH <= FDRThreshold)] <- "brown"
border.vc <- c (z_set1.col)
z_set1_U.col[which (z_set1.df$FDR_BH_U <= FDRThreshold)] <- "brown"
border_U.vc <- c (z_set1_U.col)
z_set1_TL.col[which (z_set1.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
border_TL.vc <- c (z_set1_TL.col)
z_set1_CNML.col[which (z_set1.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border_CNML.vc <- c (z_set1_CNML.col)
nc.vc <- z_set1.col
nc_U.vc <- z_set1_U.col
nc_TL.vc <- z_set1_TL.col
nc_CNML.vc <- z_set1_CNML.col
} else if (Kl == "NO"){
z_set2.col <- rep ("gray30", length (z_set.gsid))
z_set2_U.col <- rep ("gray30", length (z_set.gsid))
z_set2_TL.col <- rep ("gray30", length (z_set.gsid))
z_set2_CNML.col <- rep ("gray30", length (z_set.gsid))
resObjectKln <- get(paste("covAll_chipAll_",cnvType,"_KLn.df",sep=""),res.ls)
z_set2.df <- resObjectKln[match (z_set.gsid, resObjectKln$GsID), ]
height_U.mx <- matrix (data = c (z_set2.df$Pvalue_U_dev_s), nrow = 1, byrow = T)
height_c.mx <- matrix (data = c (z_set2.df$Coeff), nrow = 1, byrow = T)
height_Uc.mx <- matrix (data = c (z_set2.df$Coeff_U), nrow = 1, byrow = T)
height_TLc.mx <- matrix (data = c (z_set2.df$Coeff_TL), nrow = 1, byrow = T)
height_CNMLc.mx <- matrix (data = c (z_set2.df$Coeff_CNML), nrow = 1, byrow = T)
z_set2.col[which (z_set2.df$FDR_BH <= FDRThreshold)] <- "brown"
border.vc <- c (z_set2.col)
z_set2_U.col[which (z_set2.df$FDR_BH_U <= FDRThreshold)] <- "brown"
border_U.vc <- c (z_set2_U.col)
z_set2_TL.col[which (z_set2.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
border_TL.vc <- c (z_set2_TL.col)
z_set2_CNML.col[which (z_set2.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border_CNML.vc <- c (z_set2_CNML.col)
nc.vc <- z_set2.col
nc_U.vc <- z_set2_U.col
nc_TL.vc <- z_set2_TL.col
nc_CNML.vc <- z_set2_CNML.col
}
# if ("no_corr" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){#GP20171012
if ("no_corr" %in% correctionViz || "ALL" %in% correctionViz){
rangeVals <- range(height_c.mx, na.rm=TRUE,finite=TRUE)
rangeVals[1] <- min(0,rangeVals[1])
rangeVals[2] <- ceiling(rangeVals[2])
pdf(paste(cnvType,"_EffectSize_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Effect Size",sep=""),
height = height_c.mx,
names.arg = z_set.labels, ylim = rangeVals, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border.vc, ncol = length (nc.vc), byrow = T)),
ylab = "Coeff")
dev.off()
}
# if ("uni_gc" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){#GP20171012
if ("uni_gc" %in% correctionViz || "ALL" %in% correctionViz){
rangeVals_U <- range(height_Uc.mx, na.rm=TRUE,finite=TRUE)
rangeVals_U[1] <- min(0,rangeVals_U[1])
rangeVals_U[2] <- ceiling(rangeVals_U[2])
pdf(paste(cnvType,"_EffectSize_U_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Effect Size: U",sep=""),
height = height_Uc.mx,
names.arg = z_set.labels, ylim = rangeVals_U, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_U.vc, ncol = length (nc_U.vc), byrow = T)),
ylab = "Coeff_U")
dev.off()
}
# if ("tot_l" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){#GP20171012
if ("tot_l" %in% correctionViz || "ALL" %in% correctionViz) {
rangeVals_TL <- range(height_TLc.mx, na.rm=TRUE,finite=TRUE)
rangeVals_TL[1] <- min(0,rangeVals_TL[1])
rangeVals_TL[2] <- ceiling(rangeVals_TL[2])
pdf(paste(cnvType,"_EffectSize_TL_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Effect Size: TL",sep=""),
height = height_TLc.mx,
names.arg = z_set.labels, ylim = rangeVals_TL, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_TL.vc, ncol = length (nc_TL.vc), byrow = T)),
ylab = "Coeff_TL")
dev.off()
}
# if ("cnvn_ml" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){#GP20171012
if ("cnvn_ml" %in% correctionViz || "ALL" %in% correctionViz){
rangeVals_CNML <- range(height_CNMLc.mx, na.rm=TRUE,finite=TRUE)
rangeVals_CNML[1] <- min(0,rangeVals_CNML[1])
rangeVals_CNML[2] <- ceiling(rangeVals_CNML[2])
pdf(paste(cnvType,"_EffectSize_CNML_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Effect Size: CNML",sep=""),
height = height_CNMLc.mx,
names.arg = z_set.labels, ylim = rangeVals_CNML, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_CNML.vc, ncol = length (nc_CNML.vc), byrow = T)),
ylab = "Coeff_CNML")
dev.off()
}
z_set.gsid <- gsList
z_set.labels <- paste (z_set.gsid, gs_len.nv[z_set.gsid], sep = ": ")
z_col.names <- c ("CASE_g1n", "CTRL_g1n", "CASE_g2n", "CTRL_g2n", "CASE_g3n", "CTRL_g3n")
pdf(paste(cnvType,"_Support_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 1)
if (Kl == "ALL"){
height_s.mx <- rbind (t (z_set1.df[, z_col.names]), t (z_set2.df[, z_col.names]))
} else if (Kl == "YES"){
height_s.mx <- t (z_set1.df[, z_col.names])
} else if (Kl == "NO"){
height_s.mx <- t (z_set2.df[, z_col.names])
}
rangeVals_s <- range(height_s.mx, na.rm=TRUE,finite=TRUE)
rangeVals_s[1] <- min(0,rangeVals_s[1])
rangeVals_s[2] <- ceiling(rangeVals_s[2])
barplot (
main = paste(cnvType,": Support",sep=""),
height = height_s.mx,
names.arg = z_set.labels, ylim = rangeVals_s, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("salmon", "skyblue"), times = length (z_set.labels)),
border = "gray30",
ylab = "CASE and CTRL subject %")
dev.off()
z_set.gsid <- gsList
z_set.labels <- paste (z_set.gsid, gs_len.nv[z_set.gsid], sep = ": ")
if (Kl == "ALL"){
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set2.col <- rep ("gray30", length (z_set.gsid))
z_set1_U.col <- rep ("gray30", length (z_set.gsid))
z_set2_U.col <- rep ("gray30", length (z_set.gsid))
z_set1_TL.col <- rep ("gray30", length (z_set.gsid))
z_set2_TL.col <- rep ("gray30", length (z_set.gsid))
z_set1_CNML.col <- rep ("gray30", length (z_set.gsid))
z_set2_CNML.col <- rep ("gray30", length (z_set.gsid))
height.mx <- matrix (data = c (z_set1.df$Pvalue_dev_s, z_set2.df$Pvalue_dev_s), nrow = 2, byrow = T)
height_U.mx <- matrix (data = c (z_set1.df$Pvalue_U_dev_s, z_set2.df$Pvalue_U_dev_s), nrow = 2, byrow = T)
height_TL.mx <- matrix (data = c (z_set1.df$Pvalue_TL_dev_s, z_set2.df$Pvalue_TL_dev_s), nrow = 2, byrow = T)
height_CNML.mx <- matrix (data = c (z_set1.df$Pvalue_CNML_dev_s, z_set2.df$Pvalue_CNML_dev_s), nrow = 2, byrow = T)
z_set1.col[which (z_set1.df$FDR_BH <= FDRThreshold)] <- "brown"
z_set2.col[which (z_set2.df$FDR_BH <= FDRThreshold)] <- "brown"
z_set1_U.col[which (z_set1.df$FDR_BH_U <= FDRThreshold)] <- "brown"
z_set2_U.col[which (z_set2.df$FDR_BH_U <= FDRThreshold)] <- "brown"
z_set1_TL.col[which (z_set1.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
z_set2_TL.col[which (z_set2.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
z_set1_CNML.col[which (z_set1.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
z_set2_CNML.col[which (z_set2.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border.vc <- c (z_set1.col, z_set2.col)
border_U.vc <- c (z_set1_U.col, z_set2_U.col)
border_TL.vc <- c (z_set1_TL.col, z_set2_TL.col)
border_CNML.vc <- c (z_set1_CNML.col, z_set2_CNML.col)
nc.vc <- z_set1.col
nc_U.vc <- z_set1_U.col
nc_TL.vc <- z_set1_TL.col
nc_CNML.vc <- z_set1_CNML.col
} else if (Kl == "YES"){
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set1_U.col <- rep ("gray30", length (z_set.gsid))
z_set1_TL.col <- rep ("gray30", length (z_set.gsid))
z_set1_CNML.col <- rep ("gray30", length (z_set.gsid))
height.mx <- matrix (data = c (z_set1.df$Pvalue_dev_s), nrow = 1, byrow = T)
height_U.mx <- matrix (data = c (z_set1.df$Pvalue_U_dev_s), nrow = 1, byrow = T)
height_TL.mx <- matrix (data = c (z_set1.df$Pvalue_TL_dev_s), nrow = 1, byrow = T)
height_CNML.mx <- matrix (data = c (z_set1.df$Pvalue_CNML_dev_s), nrow = 1, byrow = T)
z_set1.col[which (z_set1.df$FDR_BH <= FDRThreshold)] <- "brown"
border.vc <- c (z_set1.col)
z_set1_U.col[which (z_set1.df$FDR_BH_U <= FDRThreshold)] <- "brown"
border_U.vc <- c (z_set1_U.col)
z_set1_TL.col[which (z_set1.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
border_TL.vc <- c (z_set1_TL.col)
z_set1_CNML.col[which (z_set1.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border_CNML.vc <- c (z_set1_CNML.col)
nc.vc <- z_set1.col
nc_U.vc <- z_set1_U.col
nc_TL.vc <- z_set1_TL.col
nc_CNML.vc <- z_set1_CNML.col
} else if (Kl == "NO"){
z_set2.col <- rep ("gray30", length (z_set.gsid))
z_set2_U.col <- rep ("gray30", length (z_set.gsid))
z_set2_TL.col <- rep ("gray30", length (z_set.gsid))
z_set2_CNML.col <- rep ("gray30", length (z_set.gsid))
height.mx <- matrix (data = c (z_set2.df$Pvalue_dev_s), nrow = 1, byrow = T)
height_U.mx <- matrix (data = c (z_set2.df$Pvalue_U_dev_s), nrow = 1, byrow = T)
height_TL.mx <- matrix (data = c (z_set2.df$Pvalue_TL_dev_s), nrow = 1, byrow = T)
height_CNML.mx <- matrix (data = c (z_set2.df$Pvalue_CNML_dev_s), nrow = 1, byrow = T)
z_set2.col[which (z_set2.df$FDR_BH <= FDRThreshold)] <- "brown"
border.vc <- c (z_set2.col)
z_set2_U.col[which (z_set2.df$FDR_BH_U <= FDRThreshold)] <- "brown"
border_U.vc <- c (z_set2_U.col)
z_set2_TL.col[which (z_set2.df$FDR_BH_TL <= FDRThreshold)] <- "brown"
border_TL.vc <- c (z_set2_TL.col)
z_set2_CNML.col[which (z_set2.df$FDR_BH_CNML <= FDRThreshold)] <- "brown"
border_CNML.vc <- c (z_set2_CNML.col)
nc.vc <- z_set2.col
nc_U.vc <- z_set2_U.col
nc_TL.vc <- z_set2_TL.col
nc_CNML.vc <- z_set2_CNML.col
}
min.n <- min (c (min (height_U.mx), min (height_TL.mx), min (height_CNML.mx)))
max.n <- max (c (max (height_U.mx), max (height_TL.mx), max (height_CNML.mx)))
if ("no_corr" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){
rangeVals <- range(height.mx, na.rm=TRUE,finite=TRUE)
rangeVals[1] <- min(0,rangeVals[1])
rangeVals[2] <- ceiling(rangeVals[2])
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set2.col <- rep ("gray30", length (z_set.gsid))
pdf(paste(cnvType,"_Significance_Compare_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Compare Significance:",sep=""),
height = height.mx,
names.arg = z_set.labels, ylim = rangeVals, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border.vc, ncol = length (nc.vc), byrow = T)),
ylab = "-Log (Dev P-value) * sign (Coeff)")
dev.off()
}
if ("uni_gc" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){
rangeVals_U <- range(height_U.mx, na.rm=TRUE,finite=TRUE)
rangeVals_U[1] <- min(0,rangeVals_U[1])
rangeVals_U[2] <- ceiling(rangeVals_U[2])
z_set1.col <- rep ("gray30", length (z_set.gsid))
z_set2.col <- rep ("gray30", length (z_set.gsid))
pdf(paste(cnvType,"_Significance_Compare_U_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Compare Significance: U",sep=""),
height = height_U.mx,
names.arg = z_set.labels, ylim = rangeVals_U, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_U.vc, ncol = length (nc_U.vc), byrow = T)),
ylab = "-Log (Dev P-value) * sign (Coeff)")
dev.off()
}
if ("tot_l" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){
rangeVals_TL <- range(height_TL.mx, na.rm=TRUE,finite=TRUE)
rangeVals_TL[1] <- min(0,rangeVals_TL[1])
rangeVals_TL[2] <- ceiling(rangeVals_TL[2])
pdf(paste(cnvType,"_Significance_Compare_TL_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Compare Significance: TL",sep=""),
height = height_TL.mx,
names.arg = z_set.labels, ylim = rangeVals_TL, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_TL.vc, ncol = length (nc_TL.vc), byrow = T)),
ylab = "-Log (Dev P-value) * sign (Coeff)")
dev.off()
}
if ("cnvn_ml" %in% correctionViz || "ALL" %in% correctionViz || length(correctionViz) == 0){
rangeVals_CNML <- range(height_CNML.mx, na.rm=TRUE,finite=TRUE)
rangeVals_CNML[1] <- min(0,rangeVals_CNML[1])
rangeVals_CNML[2] <- ceiling(rangeVals_CNML[2])
pdf(paste(cnvType,"_Significance_Compare_CNML_",timestamp,".pdf",sep=""))
par (mar = c (plotHeight, 4, 4, 2), mgp=c(3,1,0), lwd = 2)
barplot (
main = paste(cnvType,": Compare Significance: CNML",sep=""),
height = height_CNML.mx,
names.arg = z_set.labels, ylim = rangeVals_CNML, cex.names = labelSize,
beside = T, las = 2, col = rep (c ("gray60", "gray90"), times = length (z_set.labels)),
border = as.character (matrix (data = border_CNML.vc, ncol = length (nc_CNML.vc), byrow = T)),
ylab = "-Log (Dev P-value) * sign (Coeff)")
dev.off()
}
}
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