Hi,
Is there any easy way to show all the bases in an AlignmentsTrack? Currently the mismatching bases can be shown as colors or letters, and I'd like to show all the bases in a similar manner. Ideally, the output would be similar to "samtools tview" with "dot view off" and "color for nucleotide".
I suppose one could edit the mismatch information at displayPars(plot$atrack,".__mismatches") but that looks really cumbersome. I had to stop as I didn't understand the relation of "stack" and "read" in that data.frame and in plot$atrack@range and plot$atrack@stacks.
Hi, Is there any easy way to show all the bases in an AlignmentsTrack? Currently the mismatching bases can be shown as colors or letters, and I'd like to show all the bases in a similar manner. Ideally, the output would be similar to "samtools tview" with "dot view off" and "color for nucleotide".
I suppose one could edit the mismatch information at
displayPars(plot$atrack,".__mismatches")but that looks really cumbersome. I had to stop as I didn't understand the relation of "stack" and "read" in that data.frame and inplot$atrack@rangeandplot$atrack@stacks.Thanks a lot in advance!
BR, Ari