Add notebook demonstrating how to use fgsea with EM

risserlin commented 4 years ago

add notebook to cytoscape workflow github modify output files to be gsea or generic compliant https://bioconductor.org/packages/release/bioc/html/fgsea.html

aaz398 commented 3 years ago

I used fgsea to perform my GSEA analysis. I want to use EnrichmentMap to visualize my results but I am seeing this error:

Could you please help? I'm uncertain what the exact parameters are for the UP and DOWN files to ensure they are EnrichmentMap compliant. Thank you

risserlin commented 3 years ago

Can you send me a sample of the output files for fgsea (just the top two or three lines of the file will be sufficient).

aaz398 commented 3 years ago

I sent the files to your email. Thank you

On Wed, Jun 30, 2021 at 11:46 AM Ruth Isserlin @.***> wrote:

Can you send me a sample of the output files for fgsea (just the top two or three lines of the file will be sufficient).

— You are receiving this because you commented. Reply to this email directly, view it on GitHub https://github.com/BaderLab/EnrichmentMapApp/issues/412#issuecomment-871517290, or unsubscribe https://github.com/notifications/unsubscribe-auth/AUVLI5P4ILHD3CFFZUAZPCTTVM36DANCNFSM4M6AHR5Q .

risserlin commented 3 years ago

Initial method - the format of the files that are coming out of fGSEA are not the same as the regular GSEA files. I would recommend converting them to generic enrichment files as opposed to changing them to the GSEA files. (There is a lot of extra info in GSEA format that can be annoying to add although it would be nice to have the NES values in your analysis) A detailed description of the file formats can be found here. https://enrichmentmap.readthedocs.io/en/latest/FileFormats.html#enrichment-results-files

yj2024 commented 7 months ago

I'm using fgsea results as well. I separated the up- and down-regulated pathway list based on NES value and used gmt file downloaded from MSigDB. I got this error below-

Screenshot 2024-04-01 at 3 55 22 PM

I'm using Cytoscape Version: 3.10 and enrichmentmap v3.3.6

My fgsea file column are like this: <html xmlns:v="urn:schemas-microsoft-com:vml" xmlns:o="urn:schemas-microsoft-com:office:office" xmlns:x="urn:schemas-microsoft-com:office:excel" xmlns="http://www.w3.org/TR/REC-html40">

| pathway | pval | padj | log2err | ES | NES | size | leadingEdge -- | -- | -- | -- | -- | -- | -- | -- | -- 1 | KEGG_MEDICUS_REFERENCE_TRANSLATION_INITIATION | 0.0001036 | 0.00043012 | 0.5384341 | 0.45868976 | 1.92531548 | 63 | RPL18A,RPL18,RPL4,RPL21,RPS10,RPS8,RPS7,RPL9,RPL24,RPS23,RPL7A,RPL35A,RPL13,RPL19,RPS17,RPS11,RPS4Y1,RPS12,RPL34,RPL28,RPL35,RPL31,RPS14,RPL36,RPL10A,RPL8,RPS3,RPS20,RPL23,RPL23A,RPL32,RPL11,RPL12,RPS28,RPS24,RPS9,RPS27,RPS25,RPL6,RPS19,RPS6,RPL37A,RPL15,RPL30

Could you please help me with this? I'm not sure where the error is rooted..

risserlin commented 7 months ago

for your fgsea results to mimic GSEA results they need to have the following columns. Your current output format is not a recognized format for EM

NAME
description GS DETAILS
SIZE
ES
NES NOM p-val
FDR q-val
FWER p-val
RANK AT MAX LEADING EDGE

Your above columns would need to be mapped as follows - NAME --> Name description --> Name
GS DETAILS --> you can put anything here SIZE --> size ES --> ES NES --> NES NOM p-val --> pval FDR q-val --> padj FWER p-val --> not used, just set to 0 RANK AT MAX --> this is used by EM but you need to calculate from your ranks file* and the leading edge in the results file. If you don't want to you can just set this to a random number but just know that the leading edge feature in EM won't be showing you the right answers.
LEADING EDGE --> leading edge

to calculate the rank at max in R you could do something like this - where current_fgsea_results are the dataframe with your gsea results and current_ranks is the dataframe with your gene to rank mapping. /calculate the rank at max fgsea returns the leading edge.
just need to extract the highest rank from set to get the rank at max/ calculated_rank_at_max <- apply(current_fgsea_results,1, FUN=function(x){ max(which(names(current_ranks) %in% unlist(x[8])))})

One last thing, it looks like the file that you outputted has the rows numbered. Make sure they you are exporting the results from R that you set rownames = FALSE

BaderLab / EnrichmentMapApp

Add notebook demonstrating how to use fgsea with EM #412