plotGSEA with max.overlap parameter

[loganylchen]

Hi there,

Thanks for developing this fantasy package. I have tried this package a lot, and I want to raise an issue about the visualization of the GSEA results.

In the 'classic' mode, if the genes are overlapped, they will only show part of the genes. May I ask if you could add a "max.overlap" to customize the number of showing in the GSEA plot.

Best, Logan

[reedliu]

Hi Logan, Thanks for your feedback. Could you please give me the testing code so I can reproduce your result?

[loganylchen]

Sure, here are my codes

kk_easy<-readRDS('test.rds')

pathways <- c("Chemokine signaling pathway", "Fatty acid beta-oxidation")
genes <- c("CCR2", "CCL5", "CCL3", "VAV1", "SLC25A20", "PNPLA2", "CPT1A", "ACAT1", "ACSL5", "ECHS1", "ACADS", "ECI1", "ACADVL", "GCDH", "FABP5" , "CD36" , "FABP4" )
g <- plotGSEA(kk_easy, plot_type = "classic", show_pathway = pathways, show_gene = genes)

Then it will plot the figure as below:

Test data were attached below: test.zip

[reedliu]

Hi, The warning issue is solved under v1.1.6. Please update the package and then try again. BTW, I noticed some genes are filtered, because they are not in both genesets.

allg = kk_easy$geneset %>%
  dplyr::filter(gs_name %in% c('Chemokine signaling pathway','Fatty acid beta-oxidation')) %>%
  dplyr::pull(entrez_gene) %>%
  genekitr::transId(transTo = 'sym') %>% dplyr::pull(symbol) %>% unique()

genes[!genes%in%allg]
# "FABP5" "CD36"  "FABP4"