## ----style-Sweave, eval=TRUE, echo=FALSE, results=tex--------------------
BiocStyle::latex()


## ----stage0, results=hide------------------------------------------------
library(immunoClust)


## ----stage1data, echo=TRUE-----------------------------------------------
data(dat.fcs)
dat.fcs


## ----stage1cluster, echo=TRUE--------------------------------------------
pars=c("FSC-A","SSC-A","FITC-A","PE-A","APC-A","APC-Cy7-A","Pacific Blue-A")
res.fcs <- cell.process(dat.fcs, parameters=pars)


## ----stage1summary, echo=TRUE--------------------------------------------
summary(res.fcs)


## ----stage1bias, echo=TRUE-----------------------------------------------
res2 <- cell.process(dat.fcs, bias=0.25)
summary(res2)


## ----stage1trans,echo=TRUE-----------------------------------------------
dat.transformed <- trans.ApplyToData(res.fcs, dat.fcs)


## ----stage1splom,fig=TRUE------------------------------------------------
splom(res.fcs, dat.transformed, N=1000)


## ----stage1plot, fig=TRUE------------------------------------------------
plot(res.fcs, data=dat.transformed, subset=c(1,2))


## ----stage2data, echo=TRUE-----------------------------------------------
data(dat.exp)
meta<-meta.process(dat.exp, meta.bias=0.3)


## ----stage2splom, fig=TRUE-----------------------------------------------
splom(meta$res.clusters, meta$dat.clusters$M, ellipse=TRUE)


## ----stage2plot, fig=TRUE------------------------------------------------
plot(meta$res.scatter, data=meta$dat.scatter$M)


## ----stage2export, echo=TRUE---------------------------------------------
tbl <- meta.numEvents(meta, out.all=FALSE)
tbl[,1:5]


## ----stage2final, fig=TRUE-----------------------------------------------
splom(meta$res.clusters, meta$dat.clusters$M, 
include=c(3,9,10,4,7,12), subset=3:7, ellipse=TRUE)


## ----sessionInfo, results=tex, print=TRUE, eval=TRUE---------------------
toLatex(sessionInfo())