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"   
    [15] "SMAD6"    "PPP1R15A" "TGIF1"    "FURIN"    "SMAD3"    "FKBP1A"   "MAP3K7"  
    [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
    In addition: Warning messages:
    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!!


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][1] that gives you some plotting. Also there is a [question][2] and another [tutorial][3] about how to interpret the graphical results.

Finally, this is an [article][4] about GSEA.

Hope this helps!


  [1]: https://bioinformatics-core-shared-training.github.io/cruk-summer-school-2018/RNASeq2018/html/06_Gene_set_testing.nb.html#gsea-analysis
  [2]: https://www.biostars.org/p/367191/
  [3]: http://software.broadinstitute.org/gsea/doc/GSEAUserGuideFrame.htmlhttp://
  [4]: https://www.pnas.org/content/102/43/15545