plotGSEA Term descriptions

[Natpod]

Hi,

Thank you for all the work you have put in in genekitr, this is a wonderful tool that give very insightful representations from my data.

I thought about a new functionality from the plotting module of the package. I think the plot enrichment function plotGSEA can benefit from plotting the descriptions or full names of the gene categories. This can be provided in a separate argument for example.

[reedliu]

Hi, glad you like it.

• For plotEnrich() function, users can directly modify the 'Description' column in the results of ORA.
  For example,

data(geneList, package = "genekitr")
id <- names(geneList)[abs(geneList) > 1.5]
logfc <- geneList[id]
gs <- geneset::getGO(org = "human",ont = "bp")
ego <- genORA(id, geneset = gs)
ego <- ego[1:10, ]

# default plot
plotEnrich(ego, plot_type = "dot")

# if user wants to combine GO id and term name, just change the "Description" column
ego$Description = paste0(ego$Hs_BP_ID,'(',ego$Description,')')
plotEnrich(ego, plot_type = "dot")

• For plotGSEA() function, I have set a parameter 'label_by' that allows users to specify whether to use the 'ID' or 'Description' column as the label for the image.
  For example,

data(geneList, package = "genekitr")
gs <- geneset::getGO(org = "human",ont = "bp")
gse <- genGSEA(genelist = geneList, geneset = gs)
# default plot
plotGSEA(gse, plot_type = "classic", show_pathway = 'GO:0006260', show_gene = 'SSRP1')

If user wants to combine GO id and term name, firstly change the "Description" column of gsea_df then specify label_by='description'

gse$gsea_df$Description = paste0(gse$gsea_df$Hs_BP_ID,' (',gse$gsea_df$Description,')')
plotGSEA(gse, plot_type = "classic", show_pathway = 'GO:0006260', show_gene = 'SSRP1',label_by = 'description')

Overall, the new feature added to the function can be obtained in version >= 1.2.2