As other users encountered as well: There is no information available on cytobands for my organism.
Specifically, I'm plotting chr12 of bosTau6 giving me an empty ideogram, which is fine.
gen <- "bosTau6" chr <- "chr12" start <- 71959908 end <- 77206892 ideoTrack <- IdeogramTrack(genome = gen, chromosome = chr) plotTracks(ideoTrack, from=start, to=end, chromosome=chr)
However, I'm now wondering whether I am able draw such information myself in Gviz IdeogramTrack.
To my understanding this can be done via its 'bands' argument, a data.frame which I created according to the instruction on the man page:
> head(bands.df) chrom chromStart chromEnd name gieStain chr12 794259 801565 R1 darkseagreen3 chr12 1570237 1579468 R2 darkseagreen3 chr12 4293517 4302535 R3 darkseagreen3 chr12 4477103 4484840 R4 darkseagreen3 chr12 4502439 4546010 R5 darkseagreen3 chr12 6351849 6374949 R6 darkseagreen3
Creating the track accordingly,
> ideoTrack2 <- IdeogramTrack(genome = gen, chromosome = chr, bands=bands) > plotTracks(ideoTrack, from=start, to=end, chromosome=chr)
keeps me running into that error:
Error in (ol + 1):ol : NA/NaN argument
I tried to fill a necessary slots with appropriate information, but still got that error:
Did I do something obvious wrong and how to resolve this?