Question

how to draw multiple heatmap from GeneOverlap

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C T ▴ 140

@c-t-5858

Last seen 2.5 years ago

United States

Hi,

Does anyone knows how to put two heatmaps (generated from GeneOverlap package) side-by-side?

These are the code to produce one heatmap:

library(GeneOverlap)
data(GeneOverlap)
gom.obj <- newGOM(hESC.ChIPSeq.list, genome.size=gs.RNASeq)
drawHeatmap(gom.obj, adj.p=TRUE, cutoff=1,  # show all.
    ncolused=5, grid.col="Blues", note.col="black")
drawHeatmap(gom.obj, log.scale=TRUE, ncolused=5)
drawHeatmap(gom.obj, what="Jaccard", ncolused=5)

Thank you in advance for your help.

GeneOverlap multiple figures heatmap • 1.2k views

ADD COMMENT • link updated 5.7 years ago by James W. MacDonald 68k • written 5.7 years ago by C T ▴ 140

score 0 · Answer 1 · 2020-02-06

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James W. MacDonald 68k

@james-w-macdonald-5106

Last seen 14 hours ago

United States

The heatmaps in GeneOverlap are generated using heatmap.2 from the gplots package, which uses base graphics. The canonical way to make side-by-side plots in base graphics is to use layout, or you could use split.screen or par(mfrow = 2). You can play around with settings to make things look less squished (which they almost certainly will, until you do so).

ADD COMMENT • link 5.7 years ago James W. MacDonald 68k

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Hi James,

Thanks for your comment. I'm not familiar with layout but I tried par(mfrow=c(1,2)) it doesn't work. This still plot the heatmaps on different pages.

ADD REPLY • link 5.7 years ago C T ▴ 140

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Ah, you know what? I forgot that heatmap.2 already calls layout, so you won't be able to do what you want, at least within R, using drawHeatmap.

An alternative would be to use ComplexHeatmap or pheatmap instead. You will probably have to figure out what drawHeatmap does, exactly, in order to generate something comparable on your own. But that's the promise and the peril of Open Source software. All the code is there and available, so you can do what you want. But only if you are willing and able to figure out how to do what you want, given what you have.

ADD REPLY • link 5.7 years ago James W. MacDonald 68k