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how many geneIDsets can be plot at maximum using gseaplot2?

Open dksldjlskdfjlsdkf opened this issue 6 months ago • 2 comments

deg<- FindMarkers( integrated_indAll, ident.1 = "Dedifferentiated cells", layer = "data", # In Seurat 5.0 test.use = "wilcox", min.pct = 0.1, logfc.threshold = 0.25, only.pos = FALSE ) deg <- data.frame(gene = rownames(deg), deg)#add gene names to deg table

deg1 <- deg k1 = (deg1$p_val_adj < 0.05)&(deg1$avg_log2FC < -0.5) k2 = (deg1$p_val_adj < 0.05)&(deg1$avg_log2FC > 0.5)

change = ifelse(k1,"down",ifelse(k2,"up","stable"))#If k1 is TRUE → "down",Else if k2 is TRUE → "up";Else→"stable" deg1$change <- change

#Gene name conversion s2e <- bitr(deg1$gene, fromType = "SYMBOL", toType = "ENTREZID", OrgDb = org.Hs.eg.db) #Human, convert to ENTREZID

deg1 <- inner_join(deg1,s2e,by=c("gene"="SYMBOL")) geneList = deg1$avg_log2FC names(geneList) = deg1$ENTREZID geneList = sort(geneList,decreasing = T)

gsea-KEGG enrichment analysis

kk_gse <- gseKEGG( #gseKEGG() Find KEGG pathways enriched across the entire ranked gene list geneList = geneList, organism = "hsa", keyType = 'kegg', minGSSize = 10, pvalueCutoff = 0.05, verbose = FALSE #The details are not displayed at runtime )

kk_gse <- DOSE::setReadable(kk_gse, OrgDb='org.Hs.eg.db',keyType='ENTREZID') #Gene ID conversion sortkk <- kk_gse[order(kk_gse$enrichmentScore, decreasing = T),] gseaplot2(kk_gse, row.names(sortkk)[1:10]) the last row works if it's less than or equals 10, but cannot be 30. What is the maximum number that it can plot? Thank you very much.

dksldjlskdfjlsdkf avatar Apr 29 '25 09:04 dksldjlskdfjlsdkf