Question: flowStats quadrantGate and Back-Gating
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gravatar for Aric Gregson
8.4 years ago by
Aric Gregson50
Aric Gregson50 wrote:
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
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ADD COMMENTlink written 8.4 years ago by Aric Gregson50
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