Question: clusterProfiler: cnetplot with interactive output
1
gravatar for olga.zaytseva
9 weeks ago by
olga.zaytseva10 wrote:

I have been using clusterProfiler, which is a very useful package for gene set analysis and visualisation. I would like to use the 'cnetplot' function to plot a network of GO terms and the related genes. However for larger networks, the automatic display can be confusing and it would be helpful to be able to move nodes around. In the past I could do this with with cnetplot(fixed=FALSE) option, but after updating R and re-installing clusterProfiler, the output remains static.

I am using R 3.5.3 with clusterProfiler v3.10.1 which I installed using Bioconductor 3.8. I have installed and loaded the 'igraph' package, and the following test code produces output in an interactive window, as desired:

library(igraph)
g <- make_ring(10)
tkplot(g)

Is there any way to make cnetplot output interactive, or is that functionality simply not available in the latest release?

Any help would be greatly appreciated!

clusterprofiler cnetplot • 232 views
ADD COMMENTlink modified 9 weeks ago by Guangchuang Yu2.2k • written 9 weeks ago by olga.zaytseva10
2
gravatar for Guangchuang Yu
9 weeks ago by
Guangchuang Yu2.2k
China/Guangzhou/Southern Medical University
Guangchuang Yu2.2k wrote:

it is indeed not available in the latest release as all the visualization methods were rewrote from scratch using ggplot2.

However, if you want to use the old methods, you can use the doseplot package.

ADD COMMENTlink written 9 weeks ago by Guangchuang Yu2.2k

Excellent, I was able to source the script from the doseplot package and generate an interactive cnetplot - thanks a lot Guangchuang!

ADD REPLYlink written 8 weeks ago by olga.zaytseva10
Please log in to add an answer.

Help
Access

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1706 users visited in the last hour