[BioC] flowStats quadrantGate and Back-Gating

[Aric Gregson]

Hello,

I have tried but have not been successful in using the quadrantGate
function in flowStats for back-gating. I would like to turn the
quadrantGate filter into a gate result as I do with other filters, but
it will not plot the results into another population.

For instance, I can create a rangeGate as shown:
> cd45rarangegate <- rangeGate(Data(wf[["Live CD3+"]]),#[c(3,4)],                             
                             stain="Qdot.605.A",
                             filterId="CD45RA",
                             plot=TRUE,
                             sd=0.2)

Then create a filter result:
> cd45rarangegate_result <- filter(Data(wf[['CD4+CD8-']]), cd45rarangegate)

Then demonstrate where these cells within the above filter result are in
a different plot:
> xyplot(`BD.Horizon.V450.A` ~ `AlexaFluor.647.A`, 
             Data(wf[['CD4+CD8-']]), 
             filter=cd45rarangegate_result,
             smooth=F, 
             pch=21, 
             alpha=0.5,
             par.settings=list(gate=list(col="purple", alpha=0.6))
             )

However, I cannot do the same with a quadrantGate. I can show one
population at a time by making a new rectangleGate filter result, but
this is not exactly what I want and is a bit of a hassle. 

Create the filter result as above:
> quadgate_cd4cd8_result <- filter(Data(wf[['Lymphs+']]), quadgate_cd4cd8)

Then try to plot as above:
> xyplot(`PE.A` ~ `Alexa.Fluor.700.A`,             
             Data(wf[['Lymphs+']]),
             smooth=F,
             pch=21,
             cex=0.4,
             filter=quadgate_cd4cd8_result
             )

This fails with 'error using packet 1 in evaluating argument 'subset' in
selecting a method for Subset'. I'm certain there is a way around this
and I have been unable to figure it out thus far. Thanks in advance for
suggestions.

Thanks, Aric

p.s. is it possible to make quadrantGate plot in a smooth=FALSE xyplot?

sessionInfo()
R version 2.12.2 (2011-02-25)
Platform: amd64-portbld-freebsd8.2 (64-bit)

locale:
[1] C

attached base packages:
 [1] grid      splines   tools     stats     graphics  grDevices utils     datasets  methods  
[10] base     

other attached packages:
 [1] plateCore_1.8.0     heR.Misc_0.0.4      IDPmisc_1.1.10      Rgraphviz_1.26.0   
 [5] graph_1.26.0        flowQ_1.9.0         latticeExtra_0.6-14 RColorBrewer_1.0-2 
 [9] parody_1.6.0        bioDist_1.20.0      KernSmooth_2.23-4   outliers_0.13-3    
[13] flowStats_1.8.0     cluster_1.13.3      mvoutlier_1.4       fda_2.2.3          
[17] zoo_1.6-4           flowViz_1.14.0      lattice_0.19-17     flowCore_1.16.0    
[21] rrcov_1.1-00        pcaPP_1.8-2         mvtnorm_0.9-92      robustbase_0.5-0-1 
[25] Biobase_2.8.0       fortunes_1.4-0     

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.10.2 DBI_0.2-5            MASS_7.3-11          RSQLite_0.9-2       
 [5] annotate_1.26.1      feature_1.2.5        geneplotter_1.26.0   ks_1.7.1            
 [9] stats4_2.12.2        tcltk_2.12.2         xtable_1.5-6