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Old 07-30-2013, 10:10 AM   #1
Location: san diego

Join Date: Jan 2012
Posts: 38
Default legend for heatmaps

I am trying to create a heat map of genes with log2foldchange values. Following is my code,

pdf("fold_change_heatmap_top_100.pdf" , height=20, width=15)
x <- as.matrix(fold_change_genes[fold_change_genes$gene %in% top_100 , c(2,3,4)])
heatmap(x, margins = c(6,6) , cexCol=2 )

But I cannot see the legend for this plot. I am not sure how draw that..Could anyone please help me? I cannot use gplots::heatmap.2 as it is not installed on the cluster I am working on yet. Please suggest something.

ashuchawla is offline   Reply With Quote
Old 07-30-2013, 10:40 AM   #2
Senior Member
Location: uk

Join Date: Mar 2009
Posts: 666
Default legend for heatmaps

have you tried typing '?heatmap' to get the help page for
the R function heatmap.

That should give you a list of the parameters you can use with heatmap().
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Old 07-30-2013, 10:45 AM   #3
Location: san diego

Join Date: Jan 2012
Posts: 38

Yes I have and it doesnt tell me anything
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Old 07-31-2013, 07:55 AM   #4
Location: Milano, Italy

Join Date: Aug 2011
Posts: 93

why don't you try

heatmap.2 in library gplots

Last edited by paolo.kunder; 07-31-2013 at 07:59 AM.
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Old 04-09-2014, 03:30 AM   #5
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Join Date: Jul 2013
Posts: 142

can somebody answer this trouble, please?
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