Alternatively, you can use Gostats (either from bioconductor or webserver). Get the p-value of enriched GOterms and plot the p-value as barplot. If you are comparing multiple stages/celllines/tissues, make a matrix for each Goterm and p-value. Then plot it a a heatmap.

You can follow this discussion: Tools To Find Gene Ontology Term Enrichment

I personally use Cytoscape with ClueGO, STRING and DAVID. I find that these usually cover my needs. Cytoscape has a fine grain control over the images with its visual styles, and I usually end up colouring the nodes as per the fold change.

After GO enrichment analysis (with DAVID or else), you can summarise and visualize the go terms with revigo. It's very easy to use and it returns also the R script used for the figures, in case you want some finer control of the output.