[BioC] flowStats Plot quadrantGate Filter Result Smooth=FALSE

[Chao-Jen Wong]

Hi, Aric

We are able to reproduce the error using GvHD dataset. When setting
smooth=FALSE and using quadrantGate or quadGate as the filter, the
xyplot function would not work. There is certainly a bug in the display
functions, and it is in our to-do list to fix it. I will let you know as
soon as we fix it.

Thanks,
Chao-Jen

On 07/29/10 18:47, Aric Gregson wrote:
> 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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>   


-- 
Chao-Jen Wong
Program in Computational Biology
Division of Public Health Sciences
Fred Hutchinson Cancer Research Center
1100 Fairview Avenue N., M1-B514
PO Box 19024
Seattle, WA 98109
206.667.4485
cwon2 at fhcrc.org