When looking at a heatmap created by DESeq2, how can I find what genes are in specific regions of interest?
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?
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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
You should be plotting standardized values, not (log)expression value. Here is why: Scaling RNA-Seq data before clustering?