## ---- echo=FALSE, results="hide", warning=FALSE---------------------------- suppressPackageStartupMessages({ library('highthroughputassays') }) ## ----echo=FALSE, results="hide", warning=FALSE----------------------------- suppressPackageStartupMessages(library(flowCore)) suppressPackageStartupMessages(library(flowStats)) suppressPackageStartupMessages(library(flowViz)) ## -------------------------------------------------------------------------- ## Load packages library(flowCore) library(flowStats) library(flowViz) # for flow data visualization ## Load data data(ITN) ITN ## -------------------------------------------------------------------------- ## Create a workflow instance and transform data using asinh wf <- workFlow(ITN) asinh <- arcsinhTransform() tl <- transformList(colnames(ITN)[3:7], asinh, transformationId = "asinh") add(wf, tl) ## -------------------------------------------------------------------------- ## Identify T-cells population lg <- lymphGate(Data(wf[["asinh"]]), channels=c("SSC", "CD3"), preselection="CD4", filterId="TCells", eval=FALSE, scale=2.5) add(wf, lg$n2gate, parent="asinh") print(xyplot(SSC ~ CD3| PatientID, wf[["TCells+"]], par.settings=list(gate=list(col="red", fill="red", alpha=0.3)))) ## ----eval=FALSE------------------------------------------------------------ # if (!"BiocManager" %in% rownames(installed.packages())) # install.packages("BiocManager") # BiocManager::install("flowCore") ## ----eval=FALSE------------------------------------------------------------ # library("flowCore") ## ----eval=FALSE------------------------------------------------------------ # browseVignettes(package="flowCore") ## ----eval=FALSE------------------------------------------------------------ # help.start() ## -------------------------------------------------------------------------- sessionInfo()