if objects are returned "invisibly" it means that they are not printed to the screen when they are not assigned to a variale.
plot_anno_scores(res, go_ids) does not print the dataframe to the console, but
stats = plot_anno_scores(res, go_ids) would store the dataframe in variable
stats as usual.
However, those values are more thought of as additional information. The familiy-wise error rates (FWER) from
go_enrich() should be reported for whether a category is enriched for candidate genes or not. The p-values from Fisher's exact test are not corrected for multiple testing!
Also, the FWER is reported for the one-sided test, i.e. you have
FWER_overrep, wheareas the Fisher's exact test in
plot_anno_scores is two-sided. It should be interpreted as a quick visual overview of how background and candidate genes are distributed in the categories and root nodes.
Currently it is not possible to manipulate the plot. If you want to add text on top of the plot you could use
text() (and maybe
locator() to find the coordinates for