[BioC] FlowViz graphics problems

[Anja Schiel]

Hi,

I am currently testing flowCore and flowViz and have encountered some
problems.

I am running :
R version 2.9.0 (2009-04-17) 
i486-pc-linux-gnu 

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

other attached packages:
[1] flowViz_1.8.0    lattice_0.17-25  flowCore_1.10.0  rrcov_0.5-01    
[5] pcaPP_1.6        mvtnorm_0.9-5    robustbase_0.4-5 Biobase_2.4.1   

loaded via a namespace (and not attached):
 [1] feature_1.2.3      graph_1.22.2       grid_2.9.0
KernSmooth_2.22-22
 [5] ks_1.6.3           latticeExtra_0.5-4 MASS_7.2-47
RColorBrewer_1.0-2
 [9] stats4_2.9.0       tools_2.9.0       


I have noticed that when I use 
xyplot(`SSC-H` ~ `FSC-H`, data = fs.trans[[1]], filter = eGate)
I get a plot with the Gate defined by eGate plotted, but when I try to
do the same with
flowPlot(fs.trans[[1]], filter = eGate)
the gate is not drawn. Since the default settings seem to be filter =
NULL (and I pass eGate to filter) and showFilter = TRUE I am wondering
if this is a glinch in the system or if my command is wrong.

Second I am somewhat confused about the plot function. When I transform
my FL-H signals with 
fs.trans <- transform('FL1-H' = asinh, 'FL2-H' = asinh) %on% fs
and then run 
plot (fs.trans[[7]], 'FL1-H', breaks=256)
I get a histogram with all my data crammed into the left corner due to
the y-axis scale that seems to be extremely large. Also the axis changes
between the files. I have tried to figure out how this function works
(checked the normal and lattice information), but I am clearly not
understanding what is the underlying set of data points that determines
the y-axis scale. I would like to know how to reduce the y-axis scale
and keep it constant between different files (at least if this is not
something totally stupid to try).

Third, I have created densityplots and noticed that the order of files
is not like the order in the phenoData info. In phenoData the files are
ordered according to their file-names (or more precise by the trailing
numbers given by CellQuest), while they are plotted in some kind of
alphabetical order in densityplot. Is it possible to pass an argument to
densityplot that will plot the files in the file-names order? And is it
also possible to have the plot in black and white and not in color?

I have also tried different gates and managed to create ellipsoid,
rectangular and n2Filter, but failed to produce a polygon gate. Could
anyone provide me with an simple example how to do that?

And a last question, how could I produce a densityplot where I have an
overaly instead of shingles for several files in one figure (such as is
often used for publications, to show the shift from unstained, isotype
control to specific staining).

Any help and suggestions would be welcome, 

Anja
-- 

Anja Schiel, PhD
Department of Anatomy
Institute of Basic Medical Sciences
University of Oslo<BR>
Po-Box 1105 Blindern
N-0317 Oslo

Domus Medica
Room 2362
Tel: +47-22851137

http://www.uio.no/sok?person=anjasc