Morning all! Just a quick question. I have a basic enrichment calculation of go terms as below:
ego2 <- enrichGO(gene = rownames(tmpGR), OrgDb = org.Mm.eg.db, keyType = 'ENSEMBL', ont = "CC", pAdjustMethod = "BH", pvalueCutoff = 0.01, qvalueCutoff = 0.05) ego2 <- setReadable(ego2, OrgDb = org.Mm.eg.db) enrichGOPlotMASSIVE <- heatplot(ego2, foldChange = geneList, showCategory = 100) dotplotFINE <- dotplot(ego2, showCategory=30) + ggtitle("dotplot for GSEA") barplotFINE <- barplot(ego2, showCategory=20) networkMASSIVE <- cnetplot(ego2, foldChange=geneList)
However, besides the dot plot and bar plot, the heatplot and cnetplot are huge. Is there something basic I can do to reduce the input into these display functions? The showCateregory in the heatplot doesn't seem to reduce what I expect it to reduce.