dot plot expression after running GSEApreranked

[EH LEE]

Hi there,

I ran my data using GSEApreranked to obtain the top 20 GO term. 

I would like to represent a GO biological process as a "dot plot" graph. 

I would like to know what tool I should use or if there is another way.

Thanks for your help!

Best,

EH

[Anthony Castanza]

Hi EH,

Unfortunately, this is not a plot that is produced by the GSEA software. You can access the GSEA results in a tabular data format from the results directory for your specific job run. The TSV files there should enable you to create these plots, however I'm unable to recommend specific software for doing so, sorry.

-Anthony

Anthony S. Castanza, PhD

Curator, Molecular Signatures Database

Mesirov Lab, Department of Medicine

University of California, San Diego

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[VG]

Hi EH,

Maybe you can use the ggplot2 package for it.

Something like this:

https://hutsons-hacks.info/diverging-dot-plot-and-lollipop-charts-plotting-variance-with-ggplot2

Regards,

Varun