--- /dev/null	Thu Jan 01 00:00:00 1970 +0000
+++ b/SMART/DiffExpAnal/DESeqTools/pairwiseScatterPlots.R	Mon Apr 29 03:20:15 2013 -0400
@@ -0,0 +1,31 @@
+# pairwiseScatterPlots
+# scatter plots for pairwise comparaisons of log counts
+
+# input : counts, target, outputName
+# output : scatter plots (pdf: allows multiple figures in one file)
+
+# created Feb 21th, 2012
+# modified Sept 27th, 2012 (pdf output file)
+# modified Oct 30th, 2012 (png)
+# Marie-Agnes Dillies
+
+
+pairwiseScatterPlots <- function( counts, target, OUT_scatterPlot, out = TRUE, pdffile = FALSE ){
+
+  if (out & !pdffile) png( OUT_scatterPlot )
+  if (pdffile) pdf( OUT_scatterPlot )
+  
+  conds <- unique(target$group)
+  # colnames(counts) <- target$label
+  
+  for (i in 1:(length(conds)-1)){
+  	for (j in (i+1):length(conds)){
+  		cond1 <- conds[i]; cond2 <- conds[j]
+		pairs( log2(counts[, which(target$group %in% c(as.character(cond1), as.character(cond2)))]+1), 
+				pch=".", cex=0.5, main = paste(cond1, cond2, sep=" vs ") )
+  	}
+  }
+
+  if (pdffile) dev.off()
+  if (out) dev.off()
+}