Question: flowStats Plot quadrantGate Filter Result Smooth=FALSE
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gravatar for Aric Gregson
9.1 years ago by
Aric Gregson270
Aric Gregson270 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
flowstats • 448 views
ADD COMMENTlink written 9.1 years ago by Aric Gregson270
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