I have a GRanges object with two metadata columns, which I plot in the same Gviz plot using the groups argument:

library(Gviz)

gr <- GRanges(seqnames = "chrI", ranges = IRanges(start = 1:6, width = 1), strand = "*",
              fw = c(0, 0, 0, 1, 2, 1.5), rev = c(1.75, 2.25, 1, 0, 0, 0))

dt1 <- DataTrack(range = gr, groups = c("fw", "rev"), col = c("red", "blue"), type = "h")

at <- GenomeAxisTrack()

plotTracks(trackList = list(at, dt1), from = 1, to = 7)

When I change the order of the groups and col vector elements, the colors in the legend get mixed up.

dt2 <- DataTrack(range = gr, groups = c("rev", "fw"), col = c("blue", "red"), type = "h")

plotTracks(trackList = list(at, dt2), from = 1, to = 7)

Is this a bug or did I miss something about how the groups and col arguments are used?

Hi, thanks for pointing that out. It should be fixed in both (release and development) versions in next few days.