| gatingset_to_flowjo {CytoML} | R Documentation |
It is a R wrapper for the docker app (https://hub.docker.com/r/rglab/gs-to-flowjo)
gatingset_to_flowjo(gs, outFile, showHidden = FALSE, docker_img = NULL, ...)
gs |
a GatingSet object or a folder contains the GatingSet archive (generated by previous |
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 |
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.
nothing
## 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)