## ----echo=FALSE, results="hide", warning=FALSE-------------------------------- suppressPackageStartupMessages({ library('highthroughputassays') }) ## ----echo=FALSE, results="hide", warning=FALSE-------------------------------- suppressPackageStartupMessages(library(flowCore)) suppressPackageStartupMessages(library(flowStats)) suppressPackageStartupMessages(library(flowWorkspace)) suppressPackageStartupMessages(library(ggcyto)) suppressPackageStartupMessages(library(scales)) ## ----------------------------------------------------------------------------- ## Load packages library(flowCore) library(flowStats) library(flowWorkspace) library(ggcyto) library(scales) ## Load data data(ITN) ITN ## ----------------------------------------------------------------------------- ## Create a workflow instance and transform data using asinh gs <- GatingSet(ITN) trans.obj <- trans_new("myAsinh", transform=asinh, inverse=sinh) tl <- transformerList(colnames(ITN)[3:7], trans.obj) gs <- transform(gs, tl) ## ----------------------------------------------------------------------------- ## Identify T-cells population lg <- lymphGate(gs_cyto_data(gs), channels=c("CD3", "SSC"), preselection="CD4", filterId="TCells", scale=2.5) gs_pop_add(gs, lg) recompute(gs) ggcyto(gs, aes(x = CD3, y = SSC)) + geom_hex(bins = 32) + geom_gate("TCells") ## ----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()