## ----设置，包括= false ------------------------------------------------------------------------------------------------------------------------------------------------------------------- knitr :: opts_chunk $ set（collapse = true，comment =“＃>”，fig.width = 8，图。------------------------------------------------------------------------------------------库（FlowMerge）## ----阶段1 -------------------------------------------------------------------------------------------------------- data(rituximab) summary(rituximab) flowClust.res <- flowClust(rituximab, varNames=c(colnames（Rituximab）[1：2]），k = 1：6，trans = 1，nu.est = 1，andandstart = 20）;## ----阶段2 ---------------------------------------------------------------------------------------------------------- plot(flowMerge:::BIC(flowClust.res), main="BIC for 1 through 5 cluster flowClust solutions",xlab="K"，ylab =“ bic”，type =“ o”）;flowclust.maxbic <-flowclust.res [[whe.max（bic（flowclust.res））]];## ----阶段3 -------------------------------------------------------------------------------------------------------------- flowclust.flowobj <-FlowObj（flowclust.maxbic，rituximab）;flowclust.merge <-Merge（flowclust.flowobj，metric =“ entropy”）; i<-fitPiecewiseLinreg(flowClust.merge); ## ----stage4-------------------------------------------------------------- par(mfrow=c(2,2)); flowClust.mergeopt<-flowClust.merge[[i]]; plot(flowClust.res[[4]],data=rituximab,main="Max BIC solution"); plot(flowClust.res[[which.max(flowMerge:::ICL(flowClust.res))]],data=rituximab,main="Max ICL solution"); plot(flowClust.mergeopt,level=0.75,pch=20,main="Merged Solution"); ## ----stage5-------------------------------------------------------------- pop<-which(apply(apply(getEstimates(flowClust.mergeopt)$locations,2,function(x)order(x,decreasing=TRUE)==2),1,all)); lymphocytes<-split(flowClust.mergeopt,population=list("lymphocytes"=pop))$lymphocytes; lymphocytes<-lymphocytes[,c(3,5)]; l.flowC<-flowClust(lymphocytes,varNames=c("FL1.H","FL3.H"),K=1:8,B=1000,B.init=100,tol=1e-5,tol.init=1e-2,randomStart=50,nu=4,nu.est=1,trans=1); ## ----stage6-------------------------------------------------------------- par(mfrow=c(2,2)); l.flowO<-flowObj(l.flowC[[which.max(flowMerge:::BIC(l.flowC))]],lymphocytes); plot(l.flowO,main="max BIC solution",new.window=F,pch=20,level=0.9); plot(flowObj(l.flowC[[which.max(flowMerge:::ICL(l.flowC))]],lymphocytes),main="max ICL solution",new.window=F,pch=20,level=0.9); l.flowM<-merge(l.flowO); i<-fitPiecewiseLinreg(l.flowM,plot=T); plot(l.flowM[[i]],new.window=F,main="Best Merged Solution",pch=20,level=0.9); ## ----stage7-------------------------------------------------------------- require(Rgraphviz) f<-ptree("l.flowM",fitPiecewiseLinreg(l.flowM)); par(mfrow=c(1,2)) f(1); f(2);