Hi @rcavalca, I'm wondering that whether the parameter "fill_order" is just for the order of the legend? Or it will also be applied to priority information. For example, if there is a region that overlap with both CDS and UTR. The fill order is c("UTR", "CDS"). Will both of them be considered or just "UTR" be considered? Thanks. 

Hello,

"fill_order" to the ordering of the bars in the bar chart, and also the legend. annotatr doesn't do a prioritization, really. It reports all the intersections of a region with annotations. So if a region is in both a UTR and CDS, it will count towards each of those categories in the bar chart. I hope that answers your question.

Raymond