Hi Aric, What you have noticed appears to be a general problem with plotting of gates with a fill color in flowViz rather than an error in the calculation of results by the lymphGate function. data(GvHD) dat <- GvHD[1:2] rgate1 <- rectangleGate("FSC-H"=c(0, 400),"SSC-H"=c(-50, 300)) ## works fine xyplot(`SSC-H` ~ `FSC-H` | Visit, data=dat, filter=rgate1)gate par.settings=list(gate=list(fill="red", alpha = 0.3)) xyplot(`SSC-H` ~ `FSC-H` | Visit, data=dat, filter=rgate1, par.settings = par.settings ) rgate2 <- !rgate1 xyplot(`SSC-H` ~ `FSC-H` | Visit, data=dat, filter= rgate2, par.settings = par.settings ) The example above illustrates the same issue where the area outside the rectangle is not correctly filled with color and perhaps needs to be fixed. Nishant On 07/30/2010 02:23 PM, Aric Gregson wrote: > 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 > > _______________________________________________ > Bioconductor mailing list > Bioconductor at stat.math.ethz.ch > https://stat.ethz.ch/mailman/listinfo/bioconductor > Search the archives: http://news.gmane.org/gmane.science.biology.informatics.conductor >