Is it possible to recreate clusterProfiler plots using my own pathway data?
1
1
Entering edit mode
4.7 years ago

Hi all,

I love the plots that are produced by clusterProfiler for summarizing a large amount of gene ontology or pathway data. But what I'm interested in doing is combining pathway data from several sources to produce a plot, rather than using the enrichGO/enrichKEGG functions built into clusterProfiler. The plot I'm trying to create using my own input data is:

clusterProfiler dotplot

In clusterProfiler, the input to this is dataframe of the format:

enter image description here

I can create a dataframe containing my "customized" pathway data, but can't get it to be recognized by the dotplot function in clusterProfiler (because it's a data frame and technically not a "compareClusterResult" object). So is there a way to coerce my data frame to a compareClusterResult object or an alternative way to do this? I'm not skilled enough to recreate something similar using ggplot2 or plotly....

Many thanks for your help - much appreciated.

Jim

clusterProfiler R gene ontology pathway dotplot • 4.9k views
ADD COMMENT
1
Entering edit mode
4.7 years ago
Guangchuang Yu ★ 2.5k

maybe you can try merge_result function, see https://guangchuangyu.github.io/2015/08/functional-enrichment-for-gtex-paper/ and corresponding source code in https://github.com/GuangchuangYu/enrichment4GTEx_clusterProfiler.

ADD COMMENT
0
Entering edit mode

Thanks Guangchuang - I'll give that a go

ADD REPLY
0
Entering edit mode

It does work! many thanks~

ADD REPLY
0
Entering edit mode

Hi, Could you tell me how you did it?

ADD REPLY
0
Entering edit mode

It doesn't work out for my data as well, any suggestions. @Guangchuang Here is my post in Bioconductor https://support.bioconductor.org/p/132369/.

ADD REPLY

Login before adding your answer.

Traffic: 1081 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6