To draw a heatmap displaying DEGs associated with a specific KEGG pathway.

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13 months ago

Biostars2200 • 0

Hello, I hope all of you having a great day.

I have difficulties drawing a heatmap displaying DEGs associated with a given KEGG pathway in R studio.

I used to conduct enrichment analysis for KEGG pathways, using 'FindAllMarkers' and 'compareCluster.'

There is a figure for reference, but the code is not available. (Reference: https://www.frontiersin.org/articles/10.3389/fmicb.2021.730892/full

enter image description here

Looking forward to getting help.

Please share expertise.

Thank you.

heatmap KEGG DEG • 821 views

ADD COMMENT • link updated 13 months ago by yhdist ▴ 70 • written 13 months ago by Biostars2200 • 0

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See this question which asks the same thing: Annotating Proteins in heatmap with 1 or more pathways using R.

ADD REPLY • link 13 months ago by Mark ★ 1.6k

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The article you shared probably generated their data through fgseaMultilevel (and then generated the plots by simply using ggplot). Is this how you generated your enrichment data?

ADD REPLY • link 13 months ago by yhdist ▴ 70

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