I am ploting the Gviz Manual example:

library(Gviz)
data(twoGroups)

dTrack <- DataTrack(twoGroups, name = "uniform")

plotTracks(dTrack, groups = rep(c("control", "treated"),
each = 3), type = c("a", "p", "confint"))

The above code is supposed to plot a figure as in page 21 of the Manual (<http://www.bioconductor.org/packages/release/bioc/vignettes/Gviz/inst/doc/Gviz.pdf>).

However, what I am getting is a plot without the area which gives the confidence interval of each group ('control' and 'case').

The "confint" type can´t be used at DataTrack function anymore? If yes, why?

Thank you very much!

I am assuming that you are trying this on a plotting device that does not support alpha transparency. If you add the alpha.confint=1 parameter to your call to plotTracks, do you see the bands then? 

This visualization does not make too much sense if not plotting with transparency since it tends to overplot anything else.

Florian