Thanks James. That worked.
Tanuja
--- On Tue, 4/7/09, James W. MacDonald <jmac...@med.umich.edu> wrote:
From: James W. MacDonald <jmac...@med.umich.edu>
Subject: Re: [R] heatmap.2 no reordering of the columns and rows
To: "Tanuja Bompada" <tanujabomp...@yahoo.com>
Cc: r-help@r-project.org
Date: Tuesday, April 7, 2009, 8:02 AM
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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>
>
>
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>
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-- James W. MacDonald, M.S.
Biostatistician
Douglas Lab
University of Michigan
Department of Human Genetics
5912 Buhl
1241 E. Catherine St.
Ann Arbor MI 48109-5618
734-615-7826
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