From 37fa1bf0cc3a559eb9d4b6c1534c0bc4bd9475df Mon Sep 17 00:00:00 2001
From: chartl <chartl@348d0f76-0448-11de-a6fe-93d51630548a>
Date: Tue, 16 Feb 2010 15:12:54 +0000
Subject: [PATCH] Added heatmap function

git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2843 348d0f76-0448-11de-a6fe-93d51630548a
---
 R/plotting_library.R | 43 +++++++++++++++++++++++++++++++++++++++++++
 1 file changed, 43 insertions(+)

diff --git a/R/plotting_library.R b/R/plotting_library.R
index e1ffc6d31..db42f75c1 100644
--- a/R/plotting_library.R
+++ b/R/plotting_library.R
@@ -45,10 +45,53 @@ PlotInterleavedRows <- function(inFile,args) {
 	pdf(paste(outFileBase,"_rplot",".pdf",sep=""))
 	matplot(evalPoints,funcVal,col=colors,lty=styles,"l",xlab=xlabel,ylab=ylabel)
 	legend("topright",funcVal[1,],lty=styles,col=colors)
+	title(main=title,outer=TRUE)
 	# save
 	dev.off()
 }
 
 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)
+
 }
\ No newline at end of file