## ----style, echo=FALSE, results='hide', message=FALSE------------------------- library(BiocStyle) library(knitr) library(flowCore) opts_chunk$set(error=FALSE, message=FALSE, warning=FALSE) knitr::opts_chunk$set(echo = TRUE) ## ---- eval = FALSE------------------------------------------------------------ # if(!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # BiocManager::install("flowSpecs") ## ----------------------------------------------------------------------------- library(flowSpecs) library(flowCore) data("unmixCtrls") unmixCtrls data('fullPanel') fullPanel[,seq(4,7)] ## ----------------------------------------------------------------------------- sampleNames(unmixCtrls) ## ----------------------------------------------------------------------------- specMat <- specMatCalc(unmixCtrls, groupNames = c("Beads_", "Dead_"), autoFluoName = "PBMC_unstained.fcs") str(specMat) ## ----------------------------------------------------------------------------- fullPanelUnmix <- specUnmix(fullPanel, specMat) fullPanelUnmix ## ----------------------------------------------------------------------------- fullPanelTrans <- arcTrans(fullPanelUnmix, transNames = colnames(fullPanelUnmix)[6:18]) par(mfrow=c(1,2)) hist(exprs(fullPanelUnmix)[,7], main = "Pre transformation", xlab = "AF700_CD4", breaks = 200) hist(exprs(fullPanelTrans)[,7], main = "Post transformation", xlab = "AF700_CD4", breaks = 200) ## ----------------------------------------------------------------------------- oneVsAllPlot(fullPanelTrans, "AF647_IgM", saveResult = FALSE) ## ----------------------------------------------------------------------------- corrMat <- corrMatCreate(specMat) ## ----------------------------------------------------------------------------- corrMat["BV650_CD56", "AF647_IgM"] <- -0.1 fullPanelCorr <- correctUnmix(fullPanelUnmix, corrMat) oneVsAllPlot(fullPanelCorr, "AF647_IgM", saveResult = FALSE) ## ----------------------------------------------------------------------------- corrMat["BV650_CD56", "AF647_IgM"] <- -0.03 fullPanelCorr <- correctUnmix(fullPanelUnmix, corrMat) oneVsAllPlot(fullPanelCorr, "AF647_IgM", saveResult = FALSE) ## ----------------------------------------------------------------------------- fullPanelFs <- flowSet(fullPanelTrans) sampleNames(fullPanelFs) <- "PBMC_full_panel_d1.fcs" ## ----------------------------------------------------------------------------- fullPanelDf <- flowSet2LongDf(fullPanelFs, idInfo = list("Tissue" = "|_full_panel_..\\.fcs", "Donor" = "...._full_panel_|\\.fcs")) str(fullPanelDf) ## ----------------------------------------------------------------------------- sessionInfo()