Adjusting the size of the visual output from cluster profiler
0
0
Entering edit mode
anthony.nash ▴ 20
@anthonynash-14843
Last seen 3.6 years ago
University of Oxford

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.

Thanks

clusterProfiler heatmap GOAnalysis • 1.9k views
ADD COMMENT

Login before adding your answer.

Traffic: 524 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6