I am trying to plot two groups within a single track using Gviz.

sample_tissue = DataTrack(data = all_beta, start = sg_tissue$start,
                            end = sg_tissue$end, chromosome = chr, 
genome = gen, name = "Tissue Beta",
                            groups = tissue_all_class, degree = .8, family = c("symmetric", "gaussian"), evaluation = 100,
                            background.title = "brown", type = c("smooth", "p"), cex.legend = 0.7,     
                            cex.title = .6, cex.axis = .6, ylim = c(0,100))

I would like to change default colours (magenta and cyan), is it possible?

I've read the manual and it describes a step involving the use of feature, and the possibility of overwriting the default fill color, but I can't sort it out.

Moreover, I would like to know if it is possible to set different alphas for different elements in the track. In this case, I would like to have alpha = 1 for the "smooth" and alpha=0.5 for the "p", for example.

Thank you for your help,

Have you tried the obvious?

dat <- matrix(runif(400), nrow=4)
dtTrack <- DataTrack(start=seq(1,1000, len=100), width=10, data=dat, chromosome=1, genome="mm9", name="random data")    
library(GenomicRanges)
gr <- GRanges(seqnames="chr1", ranges=IRanges(seq(1,1000, len=100), width=10))
values(gr) <- t(dat)
dtTrack <- DataTrack(range=gr, genome="mm9", name="random data", groups=c(1,1,2,2), col=c("red", "orange"), degree = .8, family = c("symmetric", "gaussian"))

plotTracks(dtTrack, type=c("smooth", "p"))​

For different alpha settings you will indeed need to use the more flexible OverlayTrack functionality.

The best workaround I've found is to use overalyed tracks, plotting for each single track only one element, being points or line. In that way the color can be specified for each track. However I am still not able to set different alphas for overlaying tracks, probably because I'm missing something.