Hi all, 

I'm using TopGO and I did the enrichment analysis with Fisher's and KS test. I found the function printGraph very interesting since you can plot in the same graph the n most significant GOterms for your analysis. 

In the results I have GOterms represented in rectangles and GOterms in circles. The rectangles means statistically significant, but do someone know what the circles means? Are they more important in the result interpretation?

Best Regards, 

Carmen 

The rectangles don't mean statistically significant - those are just the terms with the N smallest p-values, where N is given by the argument to 'firstSigNodes'. As an example, compare

library(topGO)
data(GOdata)
data(results.tGO)
showSigOfNodes(GOdata, score(resultFisher), firstSigNodes = 5, useInfo = 'all')

showSigOfNodes(GOdata, score(resultFisher), firstSigNodes = 25, useInfo = 'all')

The colors of the plotting glyphs indicate significance, whereas the shapes are only indicative of the number of rectangles you have specified.