Author: Mike Jiang

# How to export a GatingSet to GatingML

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.

## Automated gating

### Load raw FCS files into GatingSet

    library(ncdfFlow)
    library(flowWorkspace)
    library(CytoML)
    dataDir <- system.file("extdata",package="flowWorkspaceData")
    #load raw FCS
    fs <- load_cytoset_from_fcs(file.path(dataDir,"CytoTrol_CytoTrol_1.fcs"))
    gs <- GatingSet(fs)

### 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.

### 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)"]
    tbl[c(8,11), gating_args:= "gate_range = c(2e3, 3e3)"]
    #write the new template to disc
    gtFile <- tempfile()
    write.csv(tbl, file = gtFile)
    ##reload the new template
    gt <- gatingTemplate(gtFile)
    #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]])

## Export to Cytobank

    outFile <- tempfile(fileext = ".xml")
    gatingset_to_cytobank(gs, outFile)

    ## [1] "/tmp/RtmpWQVJ5S/file15bf15ddbceb.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.

## Export to FlowJo

    outFile <- tempfile(fileext = ".wsp")
    gatingset_to_flowjo(gs, outFile)

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.