Hi,

I have read through the Gviz vignette extensively. I have two data tracks (dot plot) in my overlay, how can I change colour of the groups from something other than the standard blue and pink?

Ideally I would be able to set the colour for each specific dot using a vector - in an overlay and also single datatrack!

Finally I also want to label specific data points.

Any help is very much appreciated, I've spent a long time reading through documentation!

Current working code (sorry, looks a bit complicated than it is!)

library(Gviz)
library(GenomicRanges)
library(GenomicFeatures)
library(gridExtra)
library(trackViewer)
library(biomaRt)

start = 700e3; end = 1e6;
chr = 1
gen = "hg19"
df1_trait = "first"
df2_trait = "second"
gtrack <- GenomeAxisTrack(col="black", fontsize=17)
df1 <- data.frame(Y=rnorm(100), BP=seq(start,end, length.out=100))
df2 <- data.frame(Y=rnorm(100), BP=seq(start,end, length.out=100))

dtrack1 <- DataTrack(data = df2$Y, start = df2$BP, end = df2$BP+1, chromosome = chr, genome = gen, groups = factor(df2_trait,levels = c(df1_trait, df2_trait)), name="Log10P", legend=TRUE)
dtrack <- DataTrack(data = df1$Y, start = df1$BP, end = df1$BP+1, chromosome = chr, genome = gen, groups = factor(df1_trait,levels = c(df1_trait, df2_trait)), name="Log10P", legend=TRUE)

overlapTracks <- OverlayTrack(trackList = list(dtrack, dtrack1), background.title = "#001f4d", legend=TRUE)

grtrack <- BiomartGeneRegionTrack(genome="hg19", chromosome=chr, start=start, end=end, name="Ensembl", transcriptAnnotation="symbol", stacking="squish", collapseTranscripts="longest", background.title="brown", background.panel = "#FFFEDB", col="black", fill="salmon", fontcolor="black")

ylims <- extendrange(range(c(values(dtrack), values(dtrack1))))

png(file="saveit.png", height=600, width=700)
plotTracks(list(overlapTracks, gtrack, grtrack), from=start, to=end, col.line=NULL, ylim=ylims, fontsize=14, groupAnnotation = "group")
dev.off()

Use the col argument. See p. 30 of the Gviz user's guide for a list of all useful arguments.