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# CytoML: A tool designed to work with openCyto to exchange gated cytometry data with third-party platforms This package is designed to import/export the hierarchical gated flow data to/from the `openCyto` framework using the standard cytometry format: `gatingML2.0` and `FCS3.0`. This package makes use of our `GatingSet` R object and data model such that imported data can easily be manipulated and visualized in R using tools like `OpenCyto` and `ggcyto`. ### INSTALLATION ```r # First, install it from bionconductor so that it will pull all the dependent packages automatically library(BiocInstalller) biocLite(openCyto) # may be older # Then, install the latest version from github using devtools package install.packages("devtools") library(devtools) #load it install_github("RGLab/flowWorkspace", ref="trunk") install_github("RGLab/openCyto", ref="trunk") ``` ### Import `gatingML` and `FCS` data from other platforms into `openCyto` ```r library(CytoML) xmlfile <- system.file("extdata/cytotrol_tcell_cytobank.xml", package = "CytoML") fcsFiles <- list.files(pattern = "CytoTrol", system.file("extdata", package = "flowWorkspaceData"), full = T) gs <- cytobank2GatingSet(xmlfile, fcsFiles) ``` ### Then you can interact with the gated data (`GatingSet`) ```r #get the first sample gh <- gs[[1]] #plot the hierarchy tree plot(gh) #show all the cell populations(/nodes) getNodes(gh) #show the population statistics getPopStats(gh) #plot the gates plotGate(gh) ``` ### Export the existing `GatingSet` from `openCyto` to `Cytobank` or `flowJo` ```r dataDir <- system.file("extdata",package="flowWorkspaceData") gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)) #Cytobank outFile <- tempfile(fileext = ".xml") GatingSet2cytobank(gs, outFile) #flowJo outFile <- tempfile(fileext = ".wsp") GatingSet2flowJo(gs, outFile) ```