Question

Sort clusterProfiler result

1

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horcsct ▴ 10

@horcsct-7344

Last seen 9.0 years ago

Iran, Islamic Republic Of

Hi,

How can I sort the clusterProfiler package results (groupGOResult object) for instance according GeneRatio in groupGO?

Thanks.

clusterProfiler sort • 4.4k views

ADD COMMENT • link updated 7.4 years ago by sghoshucla • 0 • written 9.2 years ago by horcsct ▴ 10

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sghoshucla • 0

@sghoshucla-13462

Last seen 7.4 years ago

How do I subset groupGO objects?

ADD COMMENT • link 7.4 years ago sghoshucla • 0

score 2 · Accepted Answer · 2015-09-08

2

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Guangchuang Yu ★ 1.2k

@guangchuang-yu-5419

Last seen 26 days ago

China/Guangzhou/Southern Medical Univer…

If for visualization, just pass order=TRUE to barplot. It will sort result based on count which is similar to geneRatio (since geneRatio = count/geneNum, and geneNum is identical).

You can use summary(groupGO_object) to export the result as a data.frame and sort it yourself if you want to do other things.

ADD COMMENT • link 9.2 years ago Guangchuang Yu ★ 1.2k

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Thanks Guangchuang Yu,

But this only sort displayed category (showCategory) not all category. I want plot 10 category with max count.

ADD REPLY • link 9.2 years ago horcsct ▴ 10

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I use showCategory to subset the result first.

Will change to order result first, follow by subsetting. Then your question can be resolved by barplot(x, showCategory=10, order=T)

In current implementation, you can use the following script:

> df = summary(x)

> term=df$ID[order(df$Count, decreasing=T)]

> barplot(x, showCategory=term[1:10], order=T)

ADD REPLY • link 9.2 years ago Guangchuang Yu ★ 1.2k