How to plot GSEA result?
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3.0 years ago
Raheleh ▴ 230

Hello there,

I did standard GSEA for my microarray expression data. As I found out GSEA tools provide GSEA plot just for top 20 of enriched pathways. How can I provide plot for other pathways which are also significantly enriched (adj-pval < 0.05) in my dataset based on GSEA?

I am trying fgsea package in r. Could anyone please bring an example here that shows, how the input should look like for plotEnrichment()? What's wrong with my input?

I want to plot for TGFb gene set and this is my script : plotEnrichment(tgfb_gene, gene_list, gseaParam = 1, ticksSize = 0.2)

so for the first argument, examplePathway I used this list:

> tgfb_gene

\$HALLMARK_TGF_BETA_SIGNALING

[1] "TGFBR1"   "SMAD7"    "TGFB1"    "SMURF2"   "SMURF1"   "BMPR2"    "SKIL"
[8] "SKI"      "ACVR1"    "PMEPA1"   "NCOR2"    "SERPINE1" "JUNB"     "SMAD1"
[22] "BMPR1A"   "CTNNB1"   "HIPK2"    "KLF10"    "BMP2"     "ENG"      "APC"
[29] "PPM1A"    "XIAP"     "CDH1"     "ID1"      "LEFTY2"   "CDKN1C"   "TRIM33"
[36] "RAB31"    "TJP1"     "SLC20A1"  "CDK9"     "ID3"      "NOG"      "ARID4B"
[43] "IFNGR2"   "ID2"      "PPP1CA"   "SPTBN1"   "WWTR1"    "BCAR3"    "THBS1"
[50] "FNTA"     "HDAC1"    "UBE2D3"   "LTBP2"    "RHOA"


and for the second argument, exampleRanks, I used a vector of the logFC (output of differential gene expression analysis), the names of vector is the name of genes. But I got this error and warnings:

Error: Aesthetics must be either length 1 or the same as the data (1): x, xend
1: In max(tops) : no non-missing arguments to max; returning -Inf
2: In min(bottoms) : no non-missing arguments to min; returning Inf
3: In max(tops) : no non-missing arguments to max; returning -Inf
4: In min(bottoms) : no non-missing arguments to min; returning Inf
5: In max(tops) : no non-missing arguments to max; returning -Inf
6: In min(bottoms) : no non-missing arguments to min; returning Inf


Is there any other ways to provide or re-plot GSEA results?

I really appreciate any help!!

GSEA plot fgsea r plotEnrichment • 5.8k views
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Entering edit mode
3.0 years ago
gabt ▴ 120

I have been working on GSEA too and I found two very interesting resources but I am not that proficient with this kind of analysis so I am still not able to interpret the plots.

However, here you can find a very nice tutorial for R that gives you some plotting. Also there is a question and another tutorial about how to interpret the graphical results.

Finally, this is an article about GSEA.

Hope this helps!

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Many thanks @gabrit. I did it. I am trying to add title for my plot. Do you know how I can do it?

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which plot of the many listed in the tutorial are you referring to?

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3.0 years ago
Barry Digby ★ 1.0k

Hi Raheleh,

Here is a link to a RNA-seq analysis where I used GSEA and fgsea. Use the following link : https://github.com/BarryD237/D-O-Connor and scroll down the markdown file until you find "fgsea". This workflow assumed you used DESeq 2.

Regards,

Barry

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Hello Barry, Thanks for this example, but this link no longer exist. Can you please help me with this ? I used it before and it was very helpful.

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Some chump deleted my github accounts. I only recovered my primary account so that workflow is no longer available.

Follow this for fgsea - https://stephenturner.github.io/deseq-to-fgsea/#using_the_fgsea_package

And this for GSEA - How to prepare .gct file for GSEA software?

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Github repo has been restored, the link should work now. Might I suggest using @KevinBlighe EnhancedVolcano package in place of the (cumbersome) volcano plot code I used.

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3.0 years ago
guillaume.rbt ▴ 990

If you are using the GUI version of GSEA you can set the number of plots that will be generated.

You have to go in "advanced fields" where there is a field "Plot graphs for the top sets of each phenotype" which sets the number of plots.