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!