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Hi
I tried the suggestions A: Create custom IdeogramTrack (Gviz) to create an Ideogram fora scaffold my custom genome, but I can't make it work.
My bands dataframe (bands.txt) looks like this:
| chrom | chromStart | chromEnd | name | gieStain |
| scaffold_1 | 1 | 7801961 | test1 | gpos25 |
| scaffold_10 | 1 | 2993488 | test10 | gpos25 |
| scaffold_22 | 1 | 1387564 | test22 | gpos25 |
Then I'm use the following for ideogram:
bands<-read.delim("bands.txt")
options(ucscChromosomeNames=FALSE)
itrack <- IdeogramTrack(genome="X",chromosome="scaffold_22",name="scaffold_22",bands=bands)
But in my final plot the scaffold does not completely show up (lining of middle part is not there).
See plot here: https://imgur.com/a/oAyFX
Anyone knows how to show the complete scaffold as a bar? If possible, I would also like to remove the word "Chromosome" before "scaffold_22" in the plot.
Any help would be much appreciated.
Putting this as a comment rather than answer, because I can't explain why it works...
Adding more data to your bands dataframe seems to do the trick:
chrom chromStart chromEnd name gieStain scaffold_1 1 7801961 test1 gpos25 scaffold_10 1 2993488 test10 gpos25 scaffold_22 1 480000 test22 gpos1 scaffold_22 480001 490000 test22 gpos1 scaffold_22 490001 1387564 test22 gpos1 bands <- read.table("~/temp.txt", h = T) options(ucscChromosomeNames=FALSE) itrack <- IdeogramTrack(genome="X",chromosome="scaffold_22",name="scaffold_22",bands=bands) plotTracks(itrack, from = 480000, to = 490000)Note: I changed the
gieStainbecause leaving it with gpos25 created an odd white triangle at the 5' end of the scaffold, again - not sure why.Regarding removing the word "chromosome" before "scaffold_22" - the
ShowIdoption of theplotTracksfunction will remove the entire "Chromosome scaffold_22" label - not sure if you can just remove chromosome.Thank you, that worked!
I don't think that the initial band definitions make any sense. Why would you define bands that all start at the same location? Gviz doesn't really check the consistency of the band definition, but rather naively tries to draw polygons. I assume that is what you are seeing. Try defining non-overlappting bands with distinct ranges.