'm new to bioinformatics, so please excuse if this is a silly question.
I need help to generate some plots using Gviz for some genome sequencing data from a parasite.
I have managed to generate the plots, but I'm struggling to set up the annotation track to show different colours for CDSs depending on the "+" or "-" strand orientation.
For this, I have tried the following:
#Set fill as a function of CDS orientation cor <- strand(aTrack) cor[cor=="+"]<-"blue" cor[cor=="-"]<-"red" #Plot plotTracks(list(gTrack,dTrack,aTrack), from=1, to=853233, fill.histogram="red", fill=cor, shape="arrow", type="hist")
And this is what I get:
I'm importing a GFF file containing only the CDSs from a original GFF file. I have also tried with the original file and the results are similar.
Please, also note that, in the AnnotationTrack, not all CDSs are represented as arrows, even though I am setting the shape as arrow.
Worst, I get mixed colouring, with no colouring of "+" and "-" strands with blue and red, respectively.
I have no idea how I can fix this!!
Thanks in advance for any help!