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Published 20 hours ago • verified publisher icon zqfang

How can I produce gsea reports for positive and negative for cytoscape?

Open daschukds opened this issue 2 years ago • 4 comments

Hello. Thanks for this great py.

I have 2 questions.

  1. How can I produce gsea reports for positive and negative for cytoscape? Desktop version of GSEA produce 'gsea_report_for_na_neg_1650562911301.tsv' and 'gsea_report_for_na_pos_1650562911301.tsv' which will be used as input for cytoscape. However, py version does not produce these files. instead, py version produce gsea_report for all pos and neg with different column names and column info. There must be an option for these.

  2. How can I produce edb file? I followed the example on https://gseapy.readthedocs.io/en/latest/gseapy_example.html#4.-GSEA-Example. This does not explain the option to make edb file. Can you help me?

Sincerely,

daschukds avatar Apr 21 '22 19:04 daschukds

  1. I think gseapy output could be used for cytoscape input, you just need to reformat it.

  2. I'm not sure why you need the edb file? You have to generate the edb file by yourself ( export the xml format file)

zqfang avatar Apr 25 '22 20:04 zqfang

Hi. I was trying to make enrichment map using cytoscape 'enrichment map'. Enrichment map in the cytoscape accepts the results from desktop version. When I used the gseapy.gsea.phenotype.report.csv from gseapy, cytoscape popped up an error message like I need to provide correct input data. I was wondering if there is a way to generate the report file that can be accepted to 'Enrichment map' in cytoscape.

Sincerely,

daschukds avatar Apr 25 '22 21:04 daschukds

GSEApy could not support to enrichmap. However, I think you could do it using networkx easy.

  • node: enriched terms
  • node_size: pvalue/fdr/nes
  • color: pvalue/fdr/nes
  • edge: any two enriched terms have more than 1 genes overlapped
  • edge_weight: number of overlapped genes of any two enriched terms

zqfang avatar Apr 27 '22 16:04 zqfang

OK. Thanks for confirming it. I will try networkx. But i wish gseapy could support enrichmap in the future because its easier to redraw the network using mouse rather than changing coordination numbers.

daschukds avatar Apr 27 '22 17:04 daschukds

Sorry. It's long overdue. Now with v1.0.1. You can export networks for cytoscape, networkx via enrichment_map function

zqfang avatar Dec 08 '22 22:12 zqfang