Draw GO tree for some GO ids with coloring

Question

[boczniak767]

Dear All,

I have done GO-enrichment analysis in goseq package in R. I have a vector with significant GO ids and I'd like to visualise it in a manner similar to this example. So significant GOs are colored and the tree is drawn to the root (for example "Biological Process").

Such graph is super easy to generate using ontologizer cli (it ouputs dot file for use in GraphViz) but this program is not appropriate for RNA-seq data analysis.

The amigo visualizer is almost good but it does not color input GOs.

Can you suggest a suitable program?

Answer 1

[txema.heredia]

clusterProfiler has several tools to draw the results:

https://yulab-smu.top/biomedical-knowledge-mining-book/enrichplot.html

Even though they require a results object from the package as input, at least some of the graph functions internally use simply the list of GOids. You can copy the code of the function and edit that chunk to use your list.

Answer 2

[jared.andrews07]

Frankly, I'd just get as close as possible and then re-color the significant terms in Illustrator or such.

genescape can do this quite effectively and has a web app that accepts GO IDs that'd make it easy. Only problem is the downloadable image is a PNG rather than SVG.

Though if you ask nice, Istvan Albert might add that functionality.

If you have lots of terms, I'd recommend using rrvgo to collapse them into more easily interpretable sets via redundancy.

[boczniak767]

Thank you all for input. jared.andrews07 - I have too many graphs to color them manually ;-).

It is not the first time when I find answer after asking for help, and here it is goatools

[Istvan Albert]

GeneScape can also output a DOT file, the text based graph format that graphviz understands.