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thomazbastiaanssen / kronos

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Plotting circular plot output of Phase Set Enrichment Analysis #2

Open yimwy opened 1 month ago

yimwy commented 1 month ago

Hi, wonderful tool!

I am looking for codes to plot circular plots similar to the outputs of Phase Set Enrichment Analysis (https://journals.sagepub.com/doi/10.1177/0748730416631895) and wondering if it can be produced using ggplot2 or kronos?

Thanks!

thomazbastiaanssen commented 1 month ago

Many thanks for your interest. I hadn't seen PSEA before, thank you for sharing! It looks like a very reasonable method to me.

Kronos is not equipped to perform the PSEA procedure itself, as it does not perform any clustering or have a way to consider overarching pathways.

However, if you already have the outcome of a PSEA in a table/data.frame and are looking for a way to plot it, ggplot2 can certainly do that. The source code of gg_kronos_circle() in kronos contains some ggplot2 code, that could be a good place to start in this case.

Best wishes, Thomaz