## ----setup, include=FALSE----------------------------------------------------- knitr::opts_chunk$set(echo = TRUE) ## ----ej0, eval = FALSE-------------------------------------------------------- # if (!requireNamespace("BiocManager", quietly = TRUE)) # install.packages("BiocManager") # # BiocManager::install("optimalFlowData") ## ----ej01, eval = TRUE-------------------------------------------------------- library(optimalFlowData) head(Cytometry1) ## ----ej1, eval = TRUE--------------------------------------------------------- database <- buildDatabase( dataset_names = paste0('Cytometry', c(2:5, 7:9, 12:17, 19, 21)), population_ids = c('Monocytes', 'CD4+CD8-', 'Mature SIg Kappa', 'TCRgd-')) ## ----ej2, echo = TRUE--------------------------------------------------------- pairs(database[[1]][,c(4, 3, 9)], col = droplevels(database[[1]][, 11])) ## ----ej3, echo = TRUE--------------------------------------------------------- help("cytometry.diagnosis") # for an explanation of the abbreviations cytometry.diagnosis