From 93d52e978cfe4f4bdc5f71e2e9a1af15ed60cf80 Mon Sep 17 00:00:00 2001
From: Holly Ruess <s185797@biohpcwsc012.biohpc.swmed.edu>
Date: Fri, 19 Apr 2019 16:03:09 -0500
Subject: [PATCH] fix for 1-deafix-heatmap
---
genect_rnaseq/dea.R | 6 ++++--
1 file changed, 4 insertions(+), 2 deletions(-)
diff --git a/genect_rnaseq/dea.R b/genect_rnaseq/dea.R
index 058dd18..3d84563 100755
--- a/genect_rnaseq/dea.R
+++ b/genect_rnaseq/dea.R
@@ -106,8 +106,9 @@ for (i in 1:a) {
if (textscale < 0.1) {
textscale <- 0.1
}
+ zscores2 = as.matrix(zscores[rowSums(!is.na(zscores))!=0, colSums(!is.na(zscores))!=0])
png(file=paste(cond[i],'_',cond[j],'.heatmap.deseq2.png',sep=""),height=768,width=1024)
- heatmap.2(zscores, col = bluered(100),Rowv = as.dendrogram(STREE), RowSideColors = col.blocks,dendrogram='row', cexCol=textscale,labCol=s$symbol,srtRow=45,srtCol=45,trace="none", margins=c(5, 5))
+ heatmap.2(zscores2, col = bluered(100),Rowv = as.dendrogram(STREE), RowSideColors = col.blocks,dendrogram='row', cexCol=textscale,labCol=s$symbol,srtRow=45,srtCol=45,trace="none", margins=c(5, 5))
legend("topright",legend=grpnames,col=rainbow(length(grpnames)),pch=20,cex=0.5)
dev.off()
}
@@ -160,8 +161,9 @@ for (i in 1:a) {
if (textscale < 0.1) {
textscale <- 0.1
}
+ zscores2 = as.matrix(zscores[rowSums(!is.na(zscores))!=0, colSums(!is.na(zscores))!=0])
png(file=paste(cond[i],'_',cond[j],'.heatmap.edgeR.png',sep=""),height=768,width=1024)
- heatmap.2(zscores, col = bluered(100),Rowv = as.dendrogram(STREE), RowSideColors = col.blocks,dendrogram='row', cexCol=textscale,labCol=s$symbol,srtRow=45,srtCol=45,trace="none", margins=c(5, 5))
+ heatmap.2(zscores2, col = bluered(100),Rowv = as.dendrogram(STREE), RowSideColors = col.blocks,dendrogram='row', cexCol=textscale,labCol=s$symbol,srtRow=45,srtCol=45,trace="none", margins=c(5, 5))
legend("topright",legend=grpnames,col=rainbow(length(grpnames)),pch=20,cex=0.5)
dev.off()
gcont <- paste(cond[j],cond[i],sep='-')
--
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