I am finishing up a collaboration for a group for whom I have been analyzing some RNA sequencing data.
I have already generated the "standard" figures for GSEA analysis, (e.g. barcode plots, leading edge heatmaps, a joyplot, and a few other things that visualize individual pathways.).
What I am looking to do now is generate another (custom) figure that summarizes the findings from several pathways at the same time. I had thought about a circos plot might work well to illustrate the connectedness of multiple pathways, but before committing to that, I wanted to ask,
Have you seen any very well-done visualizations of gene set enrichment analyses; in particular, something that summarizes results from tests of multiple pathways of interest at the same time?
I am familiar with a variety of tools in R python bash etc.; I do not mind if the right figure is not easy to generate as long as it really pops. Thank you for your time.
In my experience people usually just pick a few individual pathways of interest and show those side by side. Couldn't you do a bar graph showing enrichment score by pathway, like is often done with GO results?
yes i can do this, however it does not address the questions as posted above.