Re-Import modified clusterProfiler's GSEA result from .csv for graphical output-generation (i.e. cnetplot, heatplot)
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6 weeks ago
NorbertK ▴ 10

Hello together,

I am currently stuck in a situation in which I am tasked to run GSEA analysis with clusterProfiler for multiple geneSets (such as Reactome, BioCarta etc.) - this has given me little to no trouble thanks to the great documentation.

Sadly my issue arises, as we are running GSEA without any cutOffs, and all the result tables, which are written to .csv files, are supposed to be merged together, filtered for significance and THEN run through plotting devices such as cnetplot and heatplot to see overlaps across multiple geneSets.

The biggest problem is that the enrichplot methods do not take dataframes as input, and rely on gseaResult or enrichResult objects to work.

I have scoured the net for a long while to find suitable solutions or internal code that could work, but I am officially at my wits end and would love to hear if others ran into similiar issues and have found a solution / work-around without having to plot manually with ggplot

TL;DR: How to re-import GSEA-derived dataframes to plot with clusterProfiler/enrichplot?

Thanks in advance!

enrichplot graphical_output GSEA clusterProfiler • 370 views
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