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Added heatmap function 

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2843 348d0f76-0448-11de-a6fe-93d51630548a
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chartl 2010-02-16 15:12:54 +00:00
parent 01af3d0663
commit 37fa1bf0cc
1 changed files with 43 additions and 0 deletions
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43
R/plotting_library.R
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@ -45,10 +45,53 @@ PlotInterleavedRows <- function(inFile,args) {
pdf(paste(outFileBase,"_rplot",".pdf",sep="")) pdf(paste(outFileBase,"_rplot",".pdf",sep=""))
matplot(evalPoints,funcVal,col=colors,lty=styles,"l",xlab=xlabel,ylab=ylabel) matplot(evalPoints,funcVal,col=colors,lty=styles,"l",xlab=xlabel,ylab=ylabel)
legend("topright",funcVal[1,],lty=styles,col=colors) legend("topright",funcVal[1,],lty=styles,col=colors)
title(main=title,outer=TRUE)
# save # save
dev.off() dev.off()
} }
PlotInterleavedRows(fileToRead,functionSpecificArgs) PlotInterleavedRows(fileToRead,functionSpecificArgs)
}
if ( functionToRun == "PlotHeatmap" ) {
### PLOT HEATMAP FUNCTION ###
#
# Normally what is meant by "heatmap" is just an image() of the
# matrix; in accordance with that, THIS FUNCTION DOES NOT COMPUTE
# DENDROGRAMS THROUGH HEATMAP(), so no rows and columns are not
# re-ordered, and dendrograms are not displayed.
#
# - expects a file of the form
#
# rentry1 \t rentry2 \t rentry3 \t ...
# colentry1 \t 0.7 \t 0.9 \t 0.4 \t ...
# colentry2 \t 0.8 \t 0.7 \t 0.6 \t ...
# ...
# Note that the rows and columns don't line up. R understands this
# and deals with it.
# Also expects an argument string:
# row_label;column_label;data_rescale_factor;plot_title;base_name_for_pdf
# - end of info -
### PLOT HEATMAP FUNCTION ###
PlotHeatmap <- function(inFile,args) {
arglist = unlist(strsplit(args,split=";"))
row_label = arglist[1]
column_label = arglist[2]
data_rescale_factor <- as.numeric(arglist[3])
plot_title = arglist[4]
base_name_for_pdf = arglist[5]
image_matrix <- data_rescale_factor*as.matrix(read.table(inFile))
## change default colors to include "cool" colors for lower end of spectrum
## e.g. red ~ near 1, yellow ~ near .75, green ~ near .5, teal ~ near .25
## blue ~ near 0
colors <- rev(rainbow(32,start=0,end=0.6,s=0.9,v=0.9,gamma=0.8))
pdf(paste(base_name_for_pdf,"_rplot",".pdf",sep=""))
heatmap(image_matrix,Rowv=NA,Colv=NA,ylab=row_label,xlab=column_label,col=colors)
title(main=plot_title,outer=TRUE)
dev.off()
}
PlotHeatmap(fileToRead,functionSpecificArgs)
} }