How to export a GatingSet to GatingML
Mike Jiang
A GatingSet object can be exported as a GatingML file or GatingML-based wsp flowJo workspace (version 10) so that they can be loaded into Cytobank or flowJo.
The GatingSet to be exported can be either parsed from Cytobank or flowJo or created by automated gating algorithms from openCtyo. Here we will demontrate the latter.
0.1 Automated gating
0.1.1 Load raw FCS files into GatingSet
library(flowWorkspace)
library(CytoML)
dataDir <- system.file("extdata",package="flowWorkspaceData")
#load raw FCS
fs <- read.ncdfFlowSet(file.path(dataDir,"CytoTrol_CytoTrol_1.fcs"))
gs <- GatingSet(fs)0.1.2 Compensate and transform
#compensate
comp <- spillover(fs[[1]])[["SPILL"]]
chnls <- colnames(comp)
comp <- compensation(comp)
gs <- compensate(gs, comp)
#transform
trans <- flowJo_biexp_trans()
trans <- transformerList(chnls, trans)
gs <- transform(gs, trans)Note that the compensation and transformation must be applied directly to GatingSet instead of flowSet/ncdfFlowSet so that these information will be stored in the GatingSet object and exported to gatingML eventually.
0.1.3 Load the gating template and run auto gating
library(openCyto)
#load the original template for tcell panel
tbl <- data.table::fread(system.file("extdata/gating_template/tcell.csv", package = "openCyto"))
#modify some paramters to fit the current data range
tbl[5, gating_args:= "gate_range = c(1e3, 3e3)"]## alias pop parent dims gating_method
## 1: nonDebris nonDebris root FSC-A mindensity
## 2: singlets singlets nonDebris FSC-A,FSC-H singletGate
## 3: lymph lymph singlets FSC-A,SSC-A flowClust
## 4: cd3 cd3 lymph CD3 mindensity
## 5: * cd4-/+cd8+/- cd3 cd4,cd8 mindensity
## 6: activated cd4 CD38+HLA+ cd4+cd8- CD38,HLA tailgate
## 7: activated cd8 CD38+HLA+ cd4-cd8+ CD38,HLA tailgate
## 8: CD45_neg CD45RA- cd4+cd8- CD45RA mindensity
## 9: CCR7_gate CCR7+ CD45_neg CCR7 flowClust
## 10: * CCR7+/-CD45RA+/- cd4+cd8- CCR7,CD45RA refGate
## 11: * CCR7+/-CD45RA+/- cd4-cd8+ CCR7,CD45RA mindensity
## gating_args collapseDataForGating groupBy
## 1: NA NA
## 2: NA NA
## 3: K=2,target=c(1e5,5e4) NA NA
## 4: TRUE 4
## 5: gate_range = c(1e3, 3e3) NA NA
## 6: NA NA
## 7: tol=0.08 NA NA
## 8: gate_range=c(2,3) NA NA
## 9: neg=1,pos=1 NA NA
## 10: CD45_neg:CCR7_gate NA NA
## 11: NA NA
## preprocessing_method preprocessing_args
## 1: NA
## 2: NA
## 3: prior_flowClust NA
## 4: NA
## 5: NA
## 6: standardize_flowset NA
## 7: standardize_flowset NA
## 8: NA
## 9: NA
## 10: NA
## 11: NAtbl[c(8,11), gating_args:= "gate_range = c(2e3, 3e3)"]## alias pop parent dims gating_method
## 1: nonDebris nonDebris root FSC-A mindensity
## 2: singlets singlets nonDebris FSC-A,FSC-H singletGate
## 3: lymph lymph singlets FSC-A,SSC-A flowClust
## 4: cd3 cd3 lymph CD3 mindensity
## 5: * cd4-/+cd8+/- cd3 cd4,cd8 mindensity
## 6: activated cd4 CD38+HLA+ cd4+cd8- CD38,HLA tailgate
## 7: activated cd8 CD38+HLA+ cd4-cd8+ CD38,HLA tailgate
## 8: CD45_neg CD45RA- cd4+cd8- CD45RA mindensity
## 9: CCR7_gate CCR7+ CD45_neg CCR7 flowClust
## 10: * CCR7+/-CD45RA+/- cd4+cd8- CCR7,CD45RA refGate
## 11: * CCR7+/-CD45RA+/- cd4-cd8+ CCR7,CD45RA mindensity
## gating_args collapseDataForGating groupBy
## 1: NA NA
## 2: NA NA
## 3: K=2,target=c(1e5,5e4) NA NA
## 4: TRUE 4
## 5: gate_range = c(1e3, 3e3) NA NA
## 6: NA NA
## 7: tol=0.08 NA NA
## 8: gate_range = c(2e3, 3e3) NA NA
## 9: neg=1,pos=1 NA NA
## 10: CD45_neg:CCR7_gate NA NA
## 11: gate_range = c(2e3, 3e3) NA NA
## preprocessing_method preprocessing_args
## 1: NA
## 2: NA
## 3: prior_flowClust NA
## 4: NA
## 5: NA
## 6: standardize_flowset NA
## 7: standardize_flowset NA
## 8: NA
## 9: NA
## 10: NA
## 11: NA#write the new template to disc
gtFile <- tempfile()
write.csv(tbl, file = gtFile)
##reload the new template
gt <- gatingTemplate(gtFile, autostart = 1L)
#run the gating
gating(gt, gs)
#hide the gates that are not of interest
toggle.helperGates(gt, gs)
#visualize the gates
library(ggcyto)
autoplot(gs[[1]])
0.2 Export to Cytobank
outFile <- tempfile(fileext = ".xml")
GatingSet2cytobank(gs, outFile)## [1] "/tmp/RtmpnmyhHX/filec58f72a95eb0.xml"Note that the resulted xml file is a standard GatingML2.0 file with some additional custom_info added so that it can be recognized by Cytobank. Here is the example gate plot from Cytobank after the gatingML is imported. 
0.3 Export to FlowJo
outFile <- tempfile(fileext = ".wsp")
GatingSet2flowJo(gs, outFile)## [1] "/tmp/RtmpnmyhHX/filec58f3a31330.wsp"The resutled wsp file is a XML-based flowJo workspace and can be loaded into flowJo(V10) along with orginal FCS files.Here is the gate plots from flowJo after it is imported. 