GO enrichment analysis graphs after goseq: any easy solutions?

Question

[Raito92]

Hello everyone! I've performed a differential gene expression analysis through Trinity, as suggested here. GO enrichment analysis was also performed through the analyze_diff_expr.pl script. The function calls the R package goseq, and as stated here, the output looks this way:

Two outputs will be generated for each set of genes tested for functional enrichment, one containing the enriched categories, and another containing the depleted categories (see .enriched and .depleted files). The .enriched file will contain those categories that are found to have enriched representation among that set of genes. Similarly, the .depleted file will contain those functional categories that are depleted (under-represented) among that very same set of target genes.

However, I don't really know how to make the classic plots you see in GO analysis, like (picked from random papers)

• Bar charts (or possibly pie charts too)
• A graph including and comparing different enrichment factors with circles
• Something hierarchical

I'm not willing to use BLAST2GO for my GO analysis, and I was wondering if there is any easy solution (like a Bioconductor R function) to use in my pipeline to process such data and plot them easily.

Thanks in advance!

[Gordon Smyth]

Cross-posted https://support.bioconductor.org/p/124909/

[Dunois]

So how did you actually visualize the goseq output in the end?

Answer 1

[Benn]

Most of the plots can be done in R (but also in other programs).

For the first you can use barplot from R.

For the second (bubble charts) you can use ggplot2.

The last figure looks like a network, which can be made with RGraphviz (or outside R with cytoscape). And a heatmap can be made with heatmap.2 from gplots.

There is not a easy solution, just get into the functions and see what you can do with it.

[afsanarupa1]

Please can you tell me details step by step how can these types of graphs be generated using output files from goseq as stated in trinity pipeline?

Thanks in advance!

Answer 2

[mks002]

Hello,

Hope you find the following tools useful in your work.

For making Bar Plot for publication, it can be done using GraphPad tool.

For Making Enrichment Plot, u can use R package clusterProfiler.

Biological Network can be done using Cyctoscape App clueGo.