How to visualize the similarity between transcriptome expression in different conditions in one heatmap ?
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8.1 years ago
jack ▴ 950

Hi,

I have transcriptome expression profile of an organism with some biological replicates in different conditions. I want to visualize the transcriptome expression similarity in different conditions in one heatmap.

Does anyone have idea how can I do that ? which metrics should I compute?

next-gen RNA-Seq R • 4.1k views
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See links here: How To Draw A Heat Map For Gene Expression Data?

http://www2.warwick.ac.uk/fac/sci/moac/people/students/peter_cock/r/heatmap/

you will need to compute pearson correlation and plot with heatmap.2

heatmap.2(m, col = hmcols, hclust = function (x) hclust(x, method = 'complete'), distfun = function (x) as.dist(1 - cor(t(x))), trace = "none", margin = c(10,6), scale = 'row', density.info = "none")

See code here: https://github.com/crazyhottommy/NGS-scripts/blob/master/DESeq_MCF7_hypoxia_RNA-seq.r

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8.1 years ago
Saad Khan ▴ 410

Check Cummerbund. I think it does what you want.

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8.1 years ago

Maybe unrelated to your question but you could get better sample relations using the package 'supraHex'. See demo: http://supfam.org/supraHex/demo-Fang.html

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