Hi Tanuja,
Tanuja Bompada wrote:
Hi,
I need to generate a heatmap on a square matrix and wouldn't want to reorder the columns and the rows on the heatmap display.
I have used the options Rowv=NULL and Colv=NULL but doesn't seem to work. Following is a snippet of the heatmap function i am using.
args <- commandArgs();
inputfile <- args[2]
imgfile <- args[3]
bitmap(imgfile, height=15, width=15, res=100, pointsize=9)
library(gplots)
library(RColorBrewer)
data <- read.table(inputfile)
matrix <- as.matrix(data)
cp <- colorRampPalette(c("red","yellow","darkgreen"),space="Lab", bias=1.5)
heatmap.2(matrix, Colv=1:ncol(matrix), dendogram="row", hclustfun=function(m)
hclust(m,method="complete"),col=cp(25),scale="none",trace="none",keysize=1,margins=c(5,12),
cexCol=1, cexRow=1)
q()
dev.off()
The alternative that i tried to avoid the reordering was
heatmap.2(matrix, Rowv=NULL, Colv=NULL, col=cp(25), scale="none", trace="none",
keysize=1, margins=c(5,12), cexCol=1, cexRow=1)
Try using Rowv = FALSE, Colv = FALSE instead of NULL. Also, add
dendrogram = "none".
Best,
Jim
But the above command doesnt generate the heatmap. So could anyone let me know what
are the options to avoid reordering the rows and columns of the heatmap and i dont
want the dendogram. I am using the R version 2.8.0 (2008-10-20)".
Thanks,
Tanuja
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