[BioC] flowStats Plot quadrantGate Filter Result Smooth=FALSE

Aric Gregson a.gregson at ucla.edu
Fri Jul 30 03:47:55 CEST 2010


Hello,

I don't believe that I have seen an explanation and I suspect that I am
not calling the filter appropriately. Using flowStats in a workFlow
with a quadrantGate making a filter I can easily plot the results with
the xyplot if smooth=TRUE (the default). However, when the populations
get small smooth=T is inadequate to visualize the results. Setting
smooth=F results in:

error in evaluating the argument 'subset' in selecting a method for
'Subset'

quad <- quadrantGate(Data(wf[["CD4+CD3+"]]),
                      stains=c("Pacific.Blue.A","Alexa.Fluor.700.A"),
                      plot=TRUE,
                      filterId="quad",
                      borderQuant=0.3,
                      alpha=c(1,1),
                      sd=c(0.6,0.6),
                      refLine.1=5,
                      refLine.2=5)
add(wf, quad, parent="CD4+CD3+")

-> This works fine:
xyplot(`Alexa.Fluor.700.A` ~ `Pacific.Blue.A` | Filename,
Data(wf[['CD4+CD3+']]), 
filter=quad)

-> This fails with the above error message:
xyplot(`Alexa.Fluor.700.A` ~ `Pacific.Blue.A` | Filename,
Data(wf[['CD4+CD3+']]), 
smooth=F,
filter=quad) -> I have tried to access gate, boundX/Y but not able

This is consistent and can be replicated with the GvHD set using a
similar filter setup.

Thanks in advance.
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] xtable_1.5-6



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