################################################### ### chunk number 1: loaddata ################################################### #line 69 "vignettes/flowTrans/inst/doc/flowTrans.Rnw" library(flowTrans) data(GvHD) transformed<-lapply(as(GvHD[1:4],"list"),function(x)flowTrans(dat=x,fun="mclMultivArcSinh",dims=c("FSC-H","SSC-H"),n2f=FALSE,parameters.only=FALSE)); ################################################### ### chunk number 2: parameters ################################################### #line 76 "vignettes/flowTrans/inst/doc/flowTrans.Rnw" parameters<-do.call(rbind,lapply(transformed,function(x)extractParams(x)[[1]])) parameters; ################################################### ### chunk number 3: plot ################################################### #line 82 "vignettes/flowTrans/inst/doc/flowTrans.Rnw" par(mfrow = c(2, 2)) plot(GvHD[[2]], c("FSC-H", "SSC-H"), main = "Untransformed sample") contour(GvHD[[2]], c("FSC-H","SSC-H"),add=TRUE); plot(transformed[[2]]$result, c("FSC-H", "SSC-H"), main = "Transformed sample") contour(transformed[[2]]$result,c("FSC-H","SSC-H"),add=TRUE); plot(GvHD[[4]], c("FSC-H", "SSC-H"), main = "Untransformed sample") contour(GvHD[[4]], c("FSC-H","SSC-H"),add=TRUE); plot(transformed[[4]]$result, c("FSC-H", "SSC-H"), main = "Transformed sample") contour(transformed[[4]]$result, c("FSC-H","SSC-H"),add=TRUE); ################################################### ### chunk number 4: multivtrans ################################################### #line 98 "vignettes/flowTrans/inst/doc/flowTrans.Rnw" transformed2<-flowTrans(dat=GvHD[[2]],fun="mclMultivArcSinh",dims=c("FSC-H","SSC-H"),n2f=FALSE,parameters.only=TRUE) transformed2