[BioC] flowViz xyplot smooth=F gate outline ONLY

[Aric Gregson]

Hello,

I am trying to use code from a presentation of Deepayan that I found
on the web. The code does a nice job a presenting density information in
the flowViz xyplot utilizing a more traditional appearance as found in
other flow software while still ploting all points. I would like to
use this as an occasional alternative to relying upon the alpha setting
to depict density. With this code, I would like to:

1) ONLY outline the gated cells rather than color and outline the
cells. I have not found a way to do this. The best I have managed is in
the example below, which overdraws with a light rose color. Setting
fill = "transparent" appears to have no effect.

2) Apply this type of plot to a flowSet. I have not figured this out
yet either. Replacing panel.xyplot.flowframe with panel.xyplot.flowset
fails.

Any hints would be greatly appreciated. 

xyplot(`Indo.1..Violet..A` ~ `APC.H7.A`, Data(wf[["logicle"]])
[[4]], 
       smooth=F,
       pch=21,
       cex=0.3,
       aspect="iso",
       panel = function(x, y, col, ...) {
         cols <-
           densCols(x, y,
                 nbin=128,
                 colramp = colori)
         panel.xyplot(x, y, col = cols, ...)
         panel.xyplot.flowframe(x, y, filter=livefilter, outline=TRUE,
		names=TRUE, col="transparent", ...) },
       par.settings=list(gate=list(col= cols, fill= cols, alpha=.9),
         gate.text=list(col="black", alpha=0.7, cex=0.6)))

Thanks in advance.

Aric
============================

R version 2.8.0 (2008-10-20) 
i386-pc-solaris2.11 

locale:
C

attached base packages:
[1] tools     stats     graphics  grDevices utils     datasets
methods [8] base     

other attached packages:
 [1] geneplotter_1.20.0  annotate_1.20.1     xtable_1.5-4       
 [4] AnnotationDbi_1.4.1 colorspace_1.0-0    flowViz_1.7.10     
 [7] lattice_0.17-20     flowCore_1.9.18     rrcov_0.4-07       
[10] robustbase_0.4-3    Biobase_2.2.1       Hmisc_3.4-4        

loaded via a namespace (and not attached):
 [1] DBI_0.2-4          KernSmooth_2.22-22 MASS_7.2-44
RColorBrewer_1.0-2 [5] RSQLite_0.7-1      cluster_1.11.11
feature_1.1-14     graph_1.20.0 [9] grid_2.8.0
latticeExtra_0.5-4 stats4_2.8.0       tcltk_2.8.0