circos.lines within the circos.genomicTrack command does not draw lines in all tracks

[Luker121]

Hi, I am using your R package, which is quite nice, but I am facing a small issue. I want to draw a genome with tracks. For this I was using the circos.genomicTrack command. As Input I have a bed file:

           chr    start      end value1 value2 value3
1 chr5 8.50e+07 8.50e+07   0.005      0       0
2 chr2 8.80e+07 8.80e+07   0.010      0       0
3 chr1 9.60e+07 9.60e+07   0.005      0       0
4 chr2 1.17e+08 1.17e+08   0.010      0       0
6 chr1 1.19e+08 1.19e+08   0.005      0       0
7 chr6 1.20e+08 1.20e+08   0.005      0       0

circos.genomicTrack(bedfiles, ylim = c(0, 1),
                    panel.fun = function(region, value, ...) {
                      circos.genomicPoints(region, value, pch = 16, cex = 1, col = c("#5CC863","#FDE725","#440154"), ...)
                      circos.lines(CELL_META$cell.xlim, c(0, 0), lty = 3, col = "#888888",lwd=0.5)
                      for(h in seq(0, 1, by = 0.2)) {
                        circos.lines(CELL_META$cell.xlim, c(h, h), lty = 3, col = "#AAAAAA",lwd=0.5)
                     }
                    }, track.height = 0.10)

I am using the code from above, but obviously it is not drawing dotted lines (within the circos.lines function) for values that do not show up in the bed file. But I want the dotted lines to be drawn for every track and not only for the tracks with values from the bed file in it. I have also attached a file with the issue I am facing (so for example in track 3 and 4 there are no dotted lines). I hope you could help me with that.

[jokergoo]

Yes, you are right, circos.genomicTrack() only adds graphics in chromsomes that are in bedfiles.

Anyway, you can first construct the track with circos.track() and draw lines in it. Laster in the same track, you use circos.genomicTrack():

circos.track(ylim = c(0, 1), panel.fun = function(x, y) {
	circos.lines(CELL_META$cell.xlim, c(0, 0), lty = 3, col = "#888888",lwd=0.5)
                      for(h in seq(0, 1, by = 0.2)) {
                        circos.lines(CELL_META$cell.xlim, c(h, h), lty = 3, col = "#AAAAAA",lwd=0.5)
                     }
})
circos.genomicTrack(bedfiles, 
                    panel.fun = function(region, value, ...) {
                      circos.genomicPoints(region, value, pch = 16, cex = 1, col = c("#5CC863","#FDE725","#440154"), ...)
                      
                    }, track.height = 0.10, track.index = get.current.track.index())

[Luker121]

Thank you very much for the provided code and sorry for opening again this issue. But now, with the new provided code I can draw a yaxis but not with a "0", even though I specified it in the argument:

circos.yaxis(side = "right", at = c(0,0.5,1), 
             sector.index = get.all.sector.index()[1], labels.cex = 0.6)

When I change the zero into a 0.1 it works, but obviously not with a zero. Is this a bug? I used the code you provided above. With my old code, it worked with setting the axis to c(0,0.5,1) (see attached pictures).

circos.yaxis(side = "right", at = c(0.1,0.5,1), 
             sector.index = get.all.sector.index()[1], labels.cex = 0.6)