From f02e94ab6f91614dfc69f45c3fa1c2a63f2a9c66 Mon Sep 17 00:00:00 2001 From: chartl Date: Tue, 16 Feb 2010 16:34:33 +0000 Subject: [PATCH] Eliminate the rescale factor -- heatmap automatically normalizes the data git-svn-id: file:///humgen/gsa-scr1/gsa-engineering/svn_contents/trunk@2845 348d0f76-0448-11de-a6fe-93d51630548a --- R/plotting_library.R | 4 ++-- 1 file changed, 2 insertions(+), 2 deletions(-) diff --git a/R/plotting_library.R b/R/plotting_library.R index db42f75c1..363a89b57 100644 --- a/R/plotting_library.R +++ b/R/plotting_library.R @@ -71,7 +71,7 @@ if ( functionToRun == "PlotHeatmap" ) { # 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 +# row_label;column_label;plot_title;base_name_for_pdf # - end of info - ### PLOT HEATMAP FUNCTION ### PlotHeatmap <- function(inFile,args) { @@ -81,7 +81,7 @@ PlotHeatmap <- function(inFile,args) { 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)) + image_matrix <- 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