I would like to plot aligned reads from a bam file over a specific region. Everything works fine with the following command:

alTrack <- AlignmentsTrack(my.bam.file, isPaired=TRUE)
snp.pos <- 308632
plotTracks(alTrack, chromosome="chr1", from=snp.pos-200, to=snp.pos+100)

But shortening the region (by increasing from) results in an error:

plotTracks(alTrack, chromosome="chr1", from=snp.pos-100, to=snp.pos+100)
Error in data.frame(x1 = start(pairGaps) - 1, y1 = gy, x2 = end(pairGaps) +  :
  arguments imply differing number of rows: 0, 1

How can I fix this?

I had the same problem too. Your reads are paired end, that's why when you plot a region that might only show one mate but not the other you get this kind of error. If you try to specify the location of the other mate, e.g. add 1500 bp upstream and downstream, you will not get this error.