enrichplot
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how many geneIDsets can be plot at maximum using gseaplot2?
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.