Specifying colors for genomicPosTransformLines

[edurand]

What is the best way to specify colors for individual posTransform lines? The following code snippet works, but does not respect the ordering of columns (i.e. the lines are colored with the wrong color)

i_track = get.cell.meta.data("track.index") 
circos.genomicPosTransformLines(bedwithcolor, track.height=0.05,
    posTransform = function(region, value) {
                        posTransform.default(region, y = 0,
                                             labels = value[[1]], 
                                             cex = 0.8, padding = 0.2, 
                                             track.index = i_track)
                   },
    direction = "outside", col=bedwithcolor$Color, lwd=2
)

[jokergoo]

Thanks for reporting this!

I will check it!

[jokergoo]

That was a bug in the code and now I have fixed it.

circos.initializeWithIdeogram()

bed = generateRandomBed(nr = 100, nc = 4)

circos.genomicPosTransformLines(bed, posTransform = posTransform.default,
    horizontalLine = "top", track.height = 0.1, 
    col = rep(1:24, times = tapply(bed[[1]], bed[[1]], length)))