After scouring the web all afternoon looking for a solution for visualising gene ontology terms, which I have already found to be over represented, I finally found a simple solution. Prior to this, I had tried several Cytoscape plugins (BiNGO, ClueGO, etc.), online webtools (REVIGO, GOrilla, WEGO, GOLEM, etc.) and others I can't be bothered posting here but to no avail.
Now the problem with most of those tools is that one needs to perform the analysis within the tool to get the graphs. I had used an independent analysis (using GOseq) to get my enriched list of GO terms. REVIGO was almost perfect for my task, except I wanted to show all my GO terms, instead of collapsing them.
So the solution to my problem was just to use AmiGO. Say these were my enriched GO terms:
First, using the "Search" function of AmiGO paste these terms into the query box and then click submit.
In the "Term Search Results", find the "Select all" button and click it. Then in the "Perform action" box, select "create a new tree with these terms as a GraphViz image" and click "go". That's it.
You can install GraphViz, export the dot file from AmiGO, open it with GraphViz and lastly export as a vector file, which can be made into a publication quality figure.
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