This vignette demonstrates how the gatingML files exported from Cytobank can be imported into R as a GatingSet object.

library(flowWorkspace)
library(CytoML)
acs <- system.file("extdata/cytobank_experiment.acs", package = "CytoML")

Create cytobank_experiment object from the ACS bundle exported from Cytobank

ce <- open_cytobank_experiment(acs)
ce
## cytobank Experiment:  tcell 
## gatingML File:  /tmp/Rtmp1qcGn2/file2cf1255c795f/experiments/3637/cytobank_gate_ml2_v41.xml 
##     panel samples
## 1 Panel 1       1

cytobank_experiment is a wrapper around the ACS file, which can be inspected by various accessors.

sampleNames(ce)
## [1] "CytoTrol_CytoTrol_1.fcs"
colnames(ce)
##  [1] "FSC-A"  "FSC-H"  "FSC-W"  "SSC-A"  "B710-A" "R660-A" "R780-A" "V450-A"
##  [9] "V545-A" "G560-A" "G780-A" "Time"
markernames(ce)
## $CytoTrol_CytoTrol_1.fcs
##  [1] "FSC-A"        "FSC-H"        "FSC-W"        "SSC-A"        "CD4"         
##  [6] "CD38 APC"     "CD8 APCH7"    "CD3"          "HLA-DR V500"  "CCR7 PE"     
## [11] "CD45RA PECy7" "Time"
pData(ce)
##                                            name Conditions Individuals
## CytoTrol_CytoTrol_1.fcs CytoTrol_CytoTrol_1.fcs condition1       ptid1

Then import cytobank_experiment into GatingSet

gs <- cytobank_to_gatingset(ce)

Alternatively, the import can be done by gatingML and fcs files that are downloaded separately form Cytobank without ACS.

xmlfile <- ce$gatingML
fcsFiles <- list.files(ce$fcsdir, full.names = TRUE)
gs <- cytobank_to_gatingset(xmlfile, fcsFiles)

However, it doesnโ€™t have the information from yaml file (part of ACS). E.g. sample tags (i.e. pData) and customized markernames. So it is recommended to import ACS.

Inspect the results

library(ggcyto)
## Plot the gates
autoplot(gs[[1]])