Hi, I am new to data analysis using R and i tried Flowcore and Flowclust so far and is very pleased with features given. I am using FlowClust to autogate the data. Where i got stuck was that i do not know how to plot log graph i.e 1) drawing a scatter graph where either or both the axis are log converted as my flowframe data is linear and i want to plot log values. Can anyone guide me in right direction as i tries the transformation as give in How to flowCore pdf but does not help. Please guide. Thanks -- output of sessionInfo(): R version 3.0.2 (2013-09-25) Platform: x86_64-w64-mingw32/x64 (64-bit) locale: [1] LC_COLLATE=English_United States.1252 LC_CTYPE=English_United States.1252 [3] LC_MONETARY=English_United States.1252 LC_NUMERIC=C [5] LC_TIME=English_United States.1252 attached base packages: [1] parallel stats graphics grDevices utils datasets methods base other attached packages: [1] flowClust_3.2.0 clue_0.3-47 corpcor_1.6.6 mnormt_1.4-7 [5] flowViz_1.26.01 lattice_0.20-23 ellipse_0.3-8 RBGL_1.38.0 [9] graph_1.40.1 Biobase_2.22.0 BiocGenerics_0.8.0 flowCore_1.28.20 loaded via a namespace (and not attached): [1] cluster_1.14.4 coda_0.16-1 feature_1.2.10 grid_3.0.2 [5] hexbin_1.26.3 IDPmisc_1.1.17 KernSmooth_2.23-10 ks_1.8.13 [9] latticeExtra_0.6-26 MASS_7.3-29 MCMCpack_1.3-3 mvtnorm_0.9-9996 [13] pcaPP_1.9-49 RColorBrewer_1.0-5 robustbase_0.9-10 rrcov_1.3-4 [17] stats4_3.0.2 tools_3.0.2 -- Sent via the guest posting facility at bioconductor.org.

Hi, Vijay, The data has to be properly transformed before you can plot it in |log| scale (no matter whether you are using |flowClust::plot| or |flowViz::xyplot| for scatter plot.) Here is the reproducible sample code: |library(parallel) library(flowClust) #load data data(GvHD) fr <- GvHD[[1]] #logicle transform trans <- estimateLogicle(fr, channels = c("FL1-H","FL3-H")) fr_trans <- transform(fr, trans) #run flowClust on the transformed data res2 <- flowClust(fr_trans, varNames=c("FL1-H","FL3-H"), K=1:6, B=100) #plot the gating result plot(res2[[3]], data=fr_trans, level=0.8, z.cutoff=0)| Mike Jiang [[alternative HTML version deleted]]