Adjusting the size of the visual output from cluster profiler
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anthony.nash ▴ 20
@anthonynash-14843
Last seen 11 months 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 • 594 views
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