clusterprofiler dotplot and cnetplot showCategory isn't working
1
0
Entering edit mode
4 months ago
pajnra ▴ 10

Hi,

I ran a KEGG overrep analysis using clusterprofiler and tried to plot them via dotplot and cnetplot but only the top two categories are showing. I've tried using showCategory and tried selecting the pathways.

enter image description here

I've tried

selected_pathways <- (Adult_KEGG$Description[1:10])

and this was the output:

selected_pathways 2 "Pyruvate metabolism" "Glucagon signaling pathway" [3] NA NA
[5] NA NA
[7] NA NA
[9] NA NA

Below is my code and output:

Adult_KEGG <- enrichKEGG(gene = Adultsig, organism = "rno",
                         pvalueCutoff = 2)
Adult_KEGG <- setReadable(Adult_KEGG, OrgDb = org.Rn.eg.db, keyType="ENTREZID")

Adultcp <- cnetplot(Adult_KEGG, shadowtext = 'none', showCategory = 5,
                    foldChange = fold_changesAdult)`

enter image description here

cnetplot dotplot clusterprofilier • 327 views
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1
Entering edit mode
4 months ago
pajnra ▴ 10

I figure it out by adjusting my qvalueCutoff.

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