## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE, results = "markup", message = FALSE, warning = FALSE) ## ----------------------------------------------------------------------------- library(flowWorkspace) library(CytoML) acs <- system.file("extdata/cytobank_experiment.acs", package = "CytoML") ## ----------------------------------------------------------------------------- ce <- open_cytobank_experiment(acs) ce ## ----------------------------------------------------------------------------- sampleNames(ce) ce_get_panels(ce) ce_get_compensations(ce) ce_get_samples(ce) ce_get_channels(ce) ce_get_markers(ce) pData(ce) ## ----------------------------------------------------------------------------- gs <- cytobank_to_gatingset(ce) ## ---- eval=FALSE-------------------------------------------------------------- # xmlfile <- ce$gatingML # fcsFiles <- list.files(ce$fcsdir, full.names = TRUE) # gs <- cytobank_to_gatingset(xmlfile, fcsFiles) ## ----------------------------------------------------------------------------- library(ggcyto) ## Plot the gates autoplot(gs[[1]]) # Extract the population statistics gs_pop_get_count_fast(gs, statType = "count")