Open MaryGoAround opened 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
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
Thanks for any idea