Hello everyone, I've performed a Gene Ontology analysis on a list of DEGs, and I obtained, as a result, a list of GO terms. For each term, it's shown how many times it's found in up and down-regulated genes. Two p-values, representing statistical significant for such findings, are given too.
I've used the function
limma in R Bioconductor.
Now I'm looking for a tool to create Gene Ontology plots.
To date, I've only created with Excel the classic 'bar plots', like these:
However, I've noticed there are more complex types of plots, like the ones where GO terms are represented by circles, whose size is proportional to their up/down regulation. Here are a couple of examples.
These plots refer to parameters not appearing in the results of my previous analysis, including a Fold enrichment, FDR and a z-score.
Is there any way to manually calculate Fold enrichment? Any suggestion in general about how to plot GO results starting from just the GO terms up and down counts and their p-values?
Thanks in advance for your help!