[BioC] Overlay Density Plot for FlowSet

[Aric Gregson]

Apologies if this is obvious or has already been discussed, but I am
struggling with how to do this from within flowCore/Viz using R 2.7.0.

I have filtered and subseted the data now that I would like to plot an
overlay density plot of a full fluorescence tube over a FMO tube and
demonstrate the positive gate. I have been able to construct a not so
interesting histogram plot as below:

plot(CD3.4.fp3Live.subset[[1]], "FL2.W", breaks=256, col=c("black"),
main="Overlay Plot FMO for CCR7\nFMO (CCR7-) Blue\nFull Fluorescent
Tube (CCR7+) Black") 
plot(CD3.4.fp3Live.subset[[5]], "FL2.W", breaks=256, col=c
("dodgerblue"), add=T)

But there is no indication of the gate and the histograms are difficult
to read in this manner. 

Another option that may work to visualize this, would be to overlay dot
plot with xyplot and show the gate somehow. But this is beyond me
currently.

Thanks for any suggestions, 

aric