## ----knitr, echo=FALSE, results="hide"---------------------------------------- library("knitr") opts_chunk$set(tidy=FALSE,dev="png",fig.show="hide", fig.width=10,fig.height=8, message=FALSE) ## ----style-knitr, eval=TRUE, echo=FALSE, results="asis"-------------------- BiocStyle::latex() ## ----loadpackage, echo=FALSE----------------------------------------------- # in order to print version number below library("flowMap") ## ----options, results='hide', echo=FALSE-------------------------------------- options(digits=3, width=80, prompt=" ", continue=" ") ## ----dataPrepExample, echo=TRUE----------------------------------------------- sam1 <- read.table(system.file("extdata/sample.txt",package="flowMap"), header=T) str(sam1) table(sam1$id) ## ----displayData-------------------------------------------------------------- sam1 <- read.table(system.file("extdata/sample.txt",package="flowMap"), header=T) sam2 <- read.table(system.file("extdata/sample.txt",package="flowMap"), header=T) table(sam1$id) table(sam2$id) ## ----makeplotSelfruns1,dev='pdf',echo=TRUE,warning=FALSE---------------------- mat1 = sam1[sam1$id==1,] mat2 = sam2[sam2$id==3,] # combine events from the two cell populations to # make pooled data mat = rbind(mat1,mat2) # sample 100 events from the pooled data sampleSize = 100 # among the 100 events, sample events from the two cell populations # such that the ratio of the cell population membership is the same # as that in the pooled data nn1 = round(sampleSize*table(mat$id)[1]/nrow(mat)) nn2 = round(sampleSize*table(mat$id)[2]/nrow(mat)) submat = rbind(mat1[sample(nrow(mat1),nn1),],mat2[sample(nrow(mat2),nn2),]) colnames(submat)[5] = "sam" # plot MST of the 100 events g1 = makeFRMST(submat) par(mar=c(0,0,0,0)) plot(g1$g,vertex.label.cex=0.01, layout=layout.fruchterman.reingold(g1$g)) ## ----makeplotSelfruns2,dev='pdf',echo=TRUE,warning=FALSE---------------------- mat1 = sam1[sam1$id==4,]; mat2 = sam2[sam2$id==5,] mat = rbind(mat1,mat2) sampleSize = 100 nn1 = round(sampleSize*table(mat$id)[1]/nrow(mat)) nn2 = round(sampleSize*table(mat$id)[2]/nrow(mat)) submat = rbind(mat1[sample(nrow(mat1),nn1),],mat2[sample(nrow(mat2),nn2),]) colnames(submat)[5] = "sam" g1 = makeFRMST(submat) par(mar=c(0,0,0,0)) plot(g1$g,vertex.label.cex=0.01,layout=layout.fruchterman.reingold(g1$g)) ## ----makeplotSelfruns3,dev='pdf',echo=TRUE,warning=FALSE---------------------- mat1 = sam1[sam1$id==6,] mat2 = sam2[sam2$id==6,] mat1$id=1; mat2$id=2 mat = rbind(mat1,mat2) sampleSize = 100 nn1 = round(sampleSize*table(mat$id)[1]/nrow(mat)) nn2 = round(sampleSize*table(mat$id)[2]/nrow(mat)) submat = rbind(mat1[sample(nrow(mat1),nn1),],mat2[sample(nrow(mat2),nn2),]) colnames(submat)[5] = "sam" g1 = makeFRMST(submat) par(mar=c(0,0,0,0)) plot(g1$g,vertex.label.cex=0.01,layout=layout.fruchterman.reingold(g1$g)) ## ----displayData2------------------------------------------------------------- sam1 <- read.table(system.file("extdata/sample.txt" ,package="flowMap"),header=T) sam2 <- read.table(system.file("extdata/sample.txt" ,package="flowMap"),header=T) table(sam1$id) table(sam2$id) ## ----compareSampleSelf,dev='pdf',warning=FALSE-------------------------------- res1 = getFRest(sam1,sam2,sampleMethod="proportional",sampleSize=100, ndraws=100,estStat="median",ncores=NULL) res1@ww library(gplots) par(mar=c(0,0,0,0)) heatmapCols <- colorRampPalette(c("red","yellow","white","blue"))(50) heatmap.2(res1@ww,trace="none",col=heatmapCols,symm=FALSE,dendrogram="none", Rowv=FALSE,Colv=FALSE,xlab="Sample 2",ylab="Sample 1") ## ----plotSelfpval,dev="pdf",echo=TRUE----------------------------------------- library(gplots) par(mar=c(0,0,0,0)) heatmapCols <- colorRampPalette(c("red","yellow","white","blue"))(50) heatmap.2(res1@pNorm,trace="none",col=heatmapCols,symm=FALSE,dendrogram="none", Rowv=FALSE,Colv=FALSE,xlab="Sample 2",ylab="Sample 1") ## ----plotSelfpvalhist,dev="pdf",echo=TRUE------------------------------------- hist(res1@pNorm,xlab="log10 p-value histogram",main="") ## ----plotMultipval,dev="pdf",echo=TRUE---------------------------------------- resMulti = makeDistmat(samples=list(sam1,sam2),sampleSize=100,ndraws=100) require(gplots) par(mar=c(0,0,0,0)) heatmapCols <- colorRampPalette(c("red","yellow","white","blue"))(50) heatmap.2(resMulti$distmat,trace="none",col=heatmapCols,symm=FALSE,dendrogram="none", Rowv=FALSE,Colv=FALSE) ## ----sessionInfo,results="asis",echo=FALSE, eval=TRUE------------------------- toLatex(sessionInfo()) ## ----resetOptions, results='hide', echo=FALSE--------------------------------- options(prompt="> ", continue="+ ") ## ----closeSockets,echo=FALSE-------------------------------------------------- closeSockets <- function() { allCon <- showConnections() socketCon <- as.integer(rownames(allCon)[allCon[, "class"] == "sockconn"]) sapply(socketCon, function(ii) close.connection(getConnection(ii)) ) } closeSockets()