Sort clusterProfiler result
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horcsct ▴ 10
@horcsct-7344
Last seen 5.9 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 • 2.3k views
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Guangchuang Yu ★ 1.2k
@guangchuang-yu-5419
Last seen 8 months 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.

 

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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.

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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)

 

 

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sghoshucla • 0
@sghoshucla-13462
Last seen 4.3 years ago

How do I subset groupGO objects?

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