It is a R wrapper for the docker app (

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



a GatingSet object or a folder contains the GatingSet archive (generated by previous save_gs call)


the workspace file path to write


whether to export hidden gates. Default is FALSE


the docker image that does the actual work


other arguments passed to save_gs




Docker images for gatingset_to_flowjo will be maintained at 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.


if (FALSE) { 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) }