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


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