Question: Adjusting the size of the visual output from cluster profiler
0
gravatar for anthony.nash
22 days ago by
University of Oxford
anthony.nash0 wrote:

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

ADD COMMENTlink written 22 days ago by anthony.nash0
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 16.09
Traffic: 277 users visited in the last hour