gatingset_to_flowjo {CytoML} | R Documentation

## Convert a GatingSet to flowJo workspace

### Description

It is a R wrapper for the docker app (https://hub.docker.com/r/rglab/gs-to-flowjo)

### Usage

    gatingset_to_flowjo(gs, outFile, showHidden = FALSE, docker_img = NULL, ...)

### Arguments

`gs` | a GatingSet object or a folder contains the GatingSet archive (generated by previous `save_gs` call)
`outFile` | the workspace file path to write
`showHidden` | whether to export hidden gates. Default is FALSE
`docker_img` | the docker image that does the actual work
`...` | other arguments passed to `save_gs`

### Details

Docker images for `gatingset_to_flowjo` will be maintained at https://hub.docker.com/r/rglab/gs-to-flowjo for the `cytolib` package version accompanying each Bioconductor release, as well as a "devel" tagged image for use with the current GitHub development braches of the RGLab cytometry packages.

If you are using CytoML from a Bioconductor release, please pull docker image corresponding to the major and minor version returned from `packageVersion("cytolib")`, For example, if `packageVersion("cytolib")` returns `2.0.2`, you should use:

`docker pull rglab/gs-to-flowjo:2.0`

If you are using CytoML from the current GitHub development branch ("master" branch), please pull the "devel" tagged image. For example:

`docker pull rglab/gs-to-flowjo:devel`

You may also specify a particular docker image and tag via the `docker_img` argument. If not provided, `gatingset_to_flowjo` will search for the correct default image corresponding to your `cytolib` version.

### Value

nothing

### Examples

    ## Not run:
    library(flowWorkspace)

    path <- system.file("extdata",package="flowWorkspaceData")
    gs_path <- list.files(path, pattern = "gs_manual",full = TRUE)
    gs <- load_gs(gs_path)

    #output to flowJo
    outFile <- tempfile(fileext = ".wsp")
    gatingset_to_flowjo(gs, outFile)

    #or directly use the archive as the input (to avoid the extra copying inside of the wrapper)
    gatingset_to_flowjo(gs_path, outFile)

    ## End(Not run)

[Package CytoML version 2.0.5 Index]