When looking at a heatmap created by DESeq2, how can I find what genes are in specific regions of interest?
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2.2 years ago
mgranada3 ▴ 30

Once I have generated my heat map and clustered the rows, how can I find out what genes are there? For example, in my image, I am interested in knowing what gene is shown as up-regulated (in red) which I squared off in my image above sample AS62.

Is there a way to make heat maps interactive? Or how can I view the gene names for certain areas?

enter image description here

pheatmap deseq2 heatmap rnaseq R • 924 views
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Look at the dataframe/matrix that was used to generate the heatmap and apply a filter rule to find which genes have fc expression of greater than say 20.

If you want an interactive pheatmap look at this: https://jokergoo.github.io/InteractiveComplexHeatmap/articles/interactivate_indirect.html

Also have you searched biostars for prev questions similar to yours? Specific gene labeling in a heatmap

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You should be plotting standardized values, not (log)expression value. Here is why: Scaling RNA-Seq data before clustering?

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2.2 years ago
fracarb8 ★ 1.7k

The clustering information is stored inside heatmap$tree_row.

tmp_heatmap <- pheatmap(...)
plot(tmp_heatmap$tree_row)

Exampl

Based on the clustering cut and the expression values, you should be able to pinpoint your genes of interest.

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