[BioC] Odd Plotting Behavior with lymphGate flowStats

[Aric Gregson]

There may be a problem with the lymphGate plot function and potentially
the entire function. While generating the lymphGate, the plot=TRUE
option shows the correct population is selected. However, when using
the non-Data() plotting technique after to show the populations (as
demonstrated in '...A typical workflow'), the wrong population is shown.
Here is an example:

lymphfilter <- lymphGate(Data(wf[["biexponential"]]),
                         channels=c("FSC.A", "SSC.A"),
                         preselection="APC.H7.A",
                         filterId="Lymphs",
                         plot=TRUE,     <- CORRECT POPULATION SHOWN
                         scale=1.8)  
add(wf, lymphfilter$n2gate, parent="biexponential")

Then:
xyplot(`FSC.A` ~ `SSC.A` | Filename, wf[['Lymphs+']]) 

Shows the wrong population. Yet, with the 'usual' Data() plotting
method the correct population is shown as within the gate:

xyplot(`FSC.A` ~ `SSC.A` | Filename, Data(wf[['biexponential']]),
       nbin=c(400,400),
       filter=lymphfilter$n2gate)

Interestingly, changing the above plot to smooth=FALSE results in the
wrong population being highlighted once again:

xyplot(`FSC.A` ~ `SSC.A` | Filename, Data(wf[['biexponential']]),
       smooth=FALSE,
       filter=lymphfilter$n2gate)

However, I have question that the correct population is gated. Based
upon the medians of each population it seems that the wrong population
may have been chosen, I'm not sure how to really know for sure.

median(exprs(Data(wf[["Lymphs-"]])[[2,"FSC.A"]]))
[1] 59620.83
> median(exprs(Data(wf[["Lymphs+"]])[[2,"FSC.A"]]))
[1] 35668.27
> median(exprs(Data(wf[["Lymphs+"]])[[1,"FSC.A"]]))
[1] 34982.41
> median(exprs(Data(wf[["Lymphs-"]])[[1,"FSC.A"]]))
[1] 62609.93

Anyone else seeing this?

Thanks, Aric

sessionInfo()
R version 2.11.0 (2010-04-22) 
amd64-portbld-freebsd8.1 

locale:
[1] C

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

other attached packages:
 [1] Rgraphviz_1.26.0    graph_1.26.0        flowQ_1.9.0        
 [4] latticeExtra_0.6-11 RColorBrewer_1.0-2  parody_1.6.0       
 [7] bioDist_1.20.0      KernSmooth_2.23-3   outliers_0.13-2    
[10] flowStats_1.7.5     cluster_1.12.3      mvoutlier_1.4      
[13] fda_2.2.2           zoo_1.6-4           flowViz_1.13.1     
[16] lattice_0.18-5      flowCore_1.15.2     rrcov_1.0-01       
[19] pcaPP_1.8-2         mvtnorm_0.9-92      robustbase_0.5-0-1 
[22] Biobase_2.8.0       fortunes_1.3-7     

loaded via a namespace (and not attached):
 [1] AnnotationDbi_1.10.2 DBI_0.2-5            MASS_7.3-5          
 [4] RSQLite_0.9-2        annotate_1.26.1      feature_1.2.4       
 [7] geneplotter_1.26.0   ks_1.6.13            stats4_2.11.0       
[10] tcltk_2.11.0         xtable_1.5-6