[BioC] Overlay Density Plot for FlowSet

[Aric Gregson]

Florian,

On Fri, 03 Oct 2008 13:31:57 -0700
Florian Hahne <fhahne at fhcrc.org> wrote:

> Let me know if that doesn't address your problem. Also please provide 
> the output of sessionInfo() in future posts, 

I thought that perhaps the drawing of gates on the densityplot, the
lack of contour() working and the fact that none of the gate outlines
are ever drawn in xyplot(smooth=F) was due to my environment, so I
upgraded. My machine environment is listed below. There was no change
in plot results. I then tried on a clean install of R 2.7.2 and the
most recent bioconductor packages (as of yesterday) for this version
of R on a Mac (sessionInfo not listed) and there was no change in plot
behavior. 

I used the same .RData and .Rhistory files on both machines, before
and after the upgrades, if that makes a difference. I must be setting up
and adding gates incorrectly or something very odd is going on. 

I have also noticed that the following example from page 7 of
'filters.pdf' produces different results depending upon which version
of the 'filters.pdf' document that I look at. 

> xyplot(`SSC-H` ~ `FSC-H` | Visit,
+        data = transform("SSC-H"=asinh,"FSC-H"=asinh) %on% GvHD,
+        subset = Patient == "6",
+        filterResults = n2gate.results,
+        filter = n2gate,
+        smooth = FALSE, alpha = 0.1)

In the filters.pdf dated March 21, 2008 the gated cells are pink and
the gate is outlined (exactly what I cannot do), but in the June 3 and
September 20 documents gated cells are black and there is not outline
of the gate dimensions (which is what I am able to do). The example that
is supposed to draw a red outlined gate in xyplot(smooth =F) follows a
similar pattern of color/no color. I have no problems getting a black
outlined gate to be drawn on the plots with xyplot(smooth=T). 

Any further suggestions would be greatly appreciated. 

thanks!

> sessionInfo()
R version 2.7.0 (2008-04-22)
i386-pc-solaris2.11

locale:
C

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

other attached packages:
 [1] flowViz_1.4.1      latticeExtra_0.5-2 lattice_0.17-15
RColorBrewer_1.0-2 [5] flowCore_1.6.0     Biobase_2.0.1
feature_1.1-13     KernSmooth_2.22-22 [9] rrcov_0.4-07
robustbase_0.4-3

loaded via a namespace (and not attached):
[1] AnnotationDbi_1.2.2 DBI_0.2-4           MASS_7.2-44
[4] RSQLite_0.7-0       geneplotter_1.18.0  grid_2.7.0
[7] stats4_2.7.0

aric
-- 
Aric Gregson <a.gregson at ucla.edu>