## ----setup, include=FALSE------------------------------------------------ library(knitr) opts_chunk$set(out.extra='style="display:block; margin: auto"', fig.align="center", message = FALSE, warning = FALSE, knitr.table.format = "markdown") assign("depthtrigger", 60, data.table:::.global) ## ----loadPackage, echo=FALSE,results='hide'------------------------------ library(flowViz) ## ----loadData------------------------------------------------------------ library(flowViz) data(GvHD) head(pData(GvHD)) ## ----subsetLattice, eval=FALSE------------------------------------------- ## xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, ## subset=Patient=="6") ## ----subsetFlowCore------------------------------------------------------ GvHD <- GvHD[pData(GvHD)$Patient==6] ## ----transform----------------------------------------------------------- tf <- transformList(from=colnames(GvHD)[3:7], tfun=asinh) GvHD <- tf %on% GvHD ## ----simpleRG, fig=TRUE, include=FALSE, echo=TRUE, prefix=FALSE, height=4.5, width=8---- rgate <- rectangleGate("FSC-H"=c(0, 400),"SSC-H"=c(-50, 300)) print(xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=rgate)) ## ----threeDRG------------------------------------------------------------ rgate2 <- rgate * rectangleGate("FL1-H"=c(2, 4)) xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=rgate2) ## ----nonSmoothScatter---------------------------------------------------- xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=rgate, smooth=FALSE) ## ----hexbinScatter------------------------------------------------------- xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=rgate, smooth=FALSE,xbin=128) ## ----plotnonSmoothScatter, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4.5, width=8---- print(plot(trellis.last.object())) ## ----nonSmoothScatterOutline--------------------------------------------- xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=rgate, smooth=FALSE, stat=TRUE,pos=0.5,abs=TRUE) ## ----multi-filters------------------------------------------------------- recGate1<-rectangleGate("FL4-H"=c(3.3,5.3),"FL2-H"=c(2.5,5)) recGate2<-rectangleGate("FL4-H"=c(4,6),"FL2-H"=c(6,8)) filters1<-filters(list(recGate1,recGate2)) xyplot(`FL2-H` ~ `FL4-H` ,data=GvHD[[1]] ,filter=filters1 ,stat=TRUE ,margin=FALSE ) ## ----plotnonSmoothScatterOutline, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4.5, width=8---- print(plot(trellis.last.object())) ## ----nonSmoothScatterOutline2-------------------------------------------- xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=rgate2, smooth=FALSE, outline=TRUE) ## ----plotnonSmoothScatter2, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4.5, width=8---- print(plot(trellis.last.object())) ## ----norm2Filter--------------------------------------------------------- n2Filter <- norm2Filter("SSC-H", "FSC-H", scale=2, filterId="Lymphocytes") n2Filter.results <- filter(GvHD, n2Filter) xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=n2Filter.results) ## ----plotnorm2Filter, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4.5, width=8---- print(plot(trellis.last.object())) ## ----curv2Filter--------------------------------------------------------- library(flowStats) c2f <- curv2Filter("FSC-H", "FL4-H", bwFac=1.8) c2f.results <- filter(GvHD, c2f) xyplot(`FL4-H` ~ `FSC-H` | Visit, data=GvHD, filter=c2f.results) ## ----plotcurv2Filter, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4.5, width=8---- print(plot(trellis.last.object())) ## ----densityplots-------------------------------------------------------- densityplot(~ `FSC-H`, GvHD, filter=curv1Filter("FSC-H")) ## ----plotdensityplots, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4.5, width=8---- print(plot(trellis.last.object())) ## ----multDensityplots---------------------------------------------------- densityplot(~ ., GvHD, channels=c("FSC-H", "SSC-H", "FL1-H"), filter=list(curv1Filter("FSC-H"), NULL, rgate2)) ## ----plotmultDensityplots, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4, width=8---- print(plot(trellis.last.object())) ## ----Pars1--------------------------------------------------------------- xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=rgate, par.settings=list(gate=list(fill="black", alpha=0.2))) ## ----plotPars1, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4.5, width=8---- print(plot(trellis.last.object())) ## ----plotPars2, eval=FALSE----------------------------------------------- ## flowViz.par.set(gate=list(fill="black", alpha=0.2)) ## xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=rgate) ## ----Pars3--------------------------------------------------------------- xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=rgate, smooth=FALSE, par.settings=list(gate=list(col="orange", alpha=0.04, pch=20, cex=0.7), flow.symbol=list(alpha=0.04, pch=20, cex=0.7))) ## ----plotPars3, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4.2, width=8---- print(plot(trellis.last.object())) ## ----Pars4--------------------------------------------------------------- xyplot(`FL4-H` ~ `FSC-H` | Visit, data=GvHD, filter=c2f.results, par.settings=list(gate=list(fill=rainbow(10), alpha=0.5, col="transparent"))) ## ----plotPars4, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4.5, width=8---- print(plot(trellis.last.object())) ## ----norm2FilterNames---------------------------------------------------- xyplot(`SSC-H` ~ `FSC-H` | Visit, data=GvHD, filter=n2Filter.results, names=TRUE, par.settings=list(gate=list(fill="black", alpha=0.2, col="transparent"), gate.text=list(col="darkred", alpha=0.7, cex=0.6))) ## ----plotnorm2FilterNames, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=4.5, width=8---- print(plot(trellis.last.object())) ## ----parCoord------------------------------------------------------------ parallel(~ . | Visit, GvHD, filter=n2Filter.results, alpha = 0.01) ## ----plotparCoord, fig=TRUE, include=FALSE, echo=FALSE, results='hide', prefix=FALSE, height=6, width=8---- print(plot(trellis.last.object()))