ClusterProfiler Ontology Bar plotting
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Entering edit mode
6.3 years ago
kalyanimeha ▴ 40

I am doing gene ontology enrichment with cluterprofiler package, and I got the result but when I plotting barplot (10000 descriptions) it's difficult to read or identify the name in the plot, is there any method to remove those descriptions which don't have any gene name.

Command Line

>ggo <- groupGO(gene     = UPT2,
+                OrgDb    = org.Hs.eg.db,
+                ont      = "MF",
+                level    = 3,   
+                readable = TRUE)

>barplot(ggo, drop=TRUE, font.size = 10,showCategory=10000, title="Up Treated2 Biological Process"
clusterprofiler Guangchuang YU dose reactomePA • 5.0k views
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6
Entering edit mode
6.3 years ago
Guangchuang Yu ★ 2.6k

is there any method to remove those descriptions which don't have any gene name.

barplot(ggo, drop=TRUE, ...)

You already know how to do it using drop=TRUE parameter.

I plotting barplot (10000 descriptions)

There is no 10000 terms in level 3 of MF.

it's difficult to read or identify the name in the plot

export the plot to file by setting large value of width and height should works.

p <- barplot(...)
ggplot2::ggsave(p, filename = your_file, width=set_a_large_value, height=set_a_large_value)
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Is there any way to plot only specific description(8-10 description) in bar plot. I had read your pdf but didn't found command for the same.

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