How to create functional categories of genes after obtaining annotation

Question

[flavobacteria]

I got the annotation done and had the full list of gene expression. So, next, I want to create a Figure like this paper (Fig. 2). What should I do? Thank you. http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0068298

[GouthamAtla]

Aren't they simple bar plots and a scatterplot with categorical variables ? Where the category is a GO "like" terms and values are vectors of fold changes of genes belongs to the category ?

You can use the appropriate tool to do a GO analysis ( or any other enrichment analysis ) to obtain this information.