clusterProfiler: cnetplot with interactive output

Question

[olga.zaytseva]

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!

[Trinh]

Hi Olga, Can we export the plot as SVG after we change it with interactive igraph? Thank you very much

Answer 1

[Guangchuang Yu]

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.

[olga.zaytseva]

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