See this :
On this page : https://wikispiral.org/tiki-index.php?page=Statistics&structure=wikispiral&page_ref_id=606
The graph colors are made using stat="identity" in ggplot2, with sorting the database in the order of the fill to have the samme color zones stacked one after another. This means that there are several layers of the same colour following each other. One option would be to adapt the data to have a proper stat="identity", with the sums of all the elements belonging to the given categories... But still I'm wondering why there is this behaviour of the output. Of course the output in rstudio doesn't show this problem.
EDIT : Actually while checking I discovered that Rstudio is as well showing the same output so I guess this is not a pluginR problem !