How do you show/export color scale of a heatmap generated by plotMRheatmap of metagenomeSeq?
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chawonhe • 0
@chawonhe-13340
Last seen 4.2 years ago

Hello!

I have used metagenomeSeq to normalize the read counts and was able to generate a heatmap. However, I cannot find a way to also show and export the color scale of the heatmap. The codes that I used for making a heatmap is just the same as in the manual document of metagenomeSeq:

trials = pData(mydata)$Farm
heatmapColColors = brewer.pal(12, "Set3")[as.integer(factor(trials))]

heatmapCols = colorRampPalette(brewer.pal(9, "RdBu"))(50) 

plotMRheatmap(obj =mydata, n = 200, cexRow = 0.4, cexCol = 0.4, trace = "none", col = heatmapCols, ColSideColors = heatmapColColors) 

Thank you in advance!

 

metagenomeseq plotmrheatmap color key • 629 views
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@james-w-macdonald-5106
Last seen 14 hours ago
United States

The plotMRheatmap function just uses heatmap.2 from the gplots package. The default is to include a color scale, so you should get one by default. For example, if I run the example code I get a heatmap with a key.

 

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chawonhe • 0
@chawonhe-13340
Last seen 4.2 years ago

Oh, I see that the color scale shows up when I do it in R. I've been working on R studio until now.

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