alexyermanos / Platypus

R package for the analysis of single-cell immune repertoires
GNU General Public License v3.0
40 stars 16 forks source link

Visualizing GSEA results #52

Open MaryGoAround opened 1 year ago

MaryGoAround commented 1 year ago

Hi

I have made a custom gene sets and I run GSEA but I really do not have any idea by Plaatypus how one could visualize the results

> gsea_EAE <- GEX_GSEA(GEX.cluster.genes.output = gene_expression_cluster[[16]], MT.Rb.filter = T, path.to.pathways = "h.all.v2023.1.Hs.symbols.gmt",Enrichment.Plots=colnames(a))
There were 50 or more warnings (use warnings() to see the first 50)
> gsea_EAE
[[1]]
# A tibble: 25 × 8
   pathway                               pval   padj log2err    ES   NES  size leadingEdge
   <chr>                                <dbl>  <dbl>   <dbl> <dbl> <dbl> <int> <list>     
 1 Stromal Factors                    0.00200 0.0286   0.432 0.729  1.91     8 <chr [6]>  
 2 Antigen Presentation               0.00229 0.0286   0.432 0.568  1.89    19 <chr [12]> 
 3 Cancer Antigen Presentation        0.00361 0.0301   0.432 0.548  1.86    20 <chr [13]> 
 4 Interferon Signaling               0.0201  0.126    0.352 0.493  1.67    20 <chr [11]> 
 5 Immune Cell Adhesion and Migration 0.0492  0.154    0.222 0.461  1.54    19 <chr [11]> 
 6 Immune Cell Localization to Tumors 0.0920  0.177    0.154 0.379  1.43    30 <chr [16]> 
 7 Myeloid Compartment                0.0487  0.154    0.277 0.843  1.40     2 <chr [2]>  
 8 NK Cell Activity                   0.150   0.268    0.138 0.626  1.31     4 <chr [3]>  
 9 Cytotoxicity                       0.172   0.287    0.123 0.511  1.28     7 <chr [2]>  
10 T-cell Priming and Activation      0.199   0.310    0.102 0.374  1.27    20 <chr [11]> 
# … with 15 more rows

Thanks for any idea