GatingHierarchy or GatingSet object, and associated flowCore gates. The data are not loaded or acted upon until an explicit call to recompute() is made on the GatingHierarchy objects in the GatingSet.
"parseWorkspace"(obj, name = NULL, execute = TRUE, isNcdf = FALSE, subset = NULL, requiregates = TRUE, includeGates = TRUE, path = obj@path, sampNloc = "keyword", ...)flowJoWorkspace to be parsed.numeric or character. The name or index of the group of samples to be imported. If NULL, the groups are printed to the screen and one can be selected interactively. Usually, multiple groups are defined in the flowJo workspace file.TRUE|FALSE a logical specifying if the gates, transformations, and compensation should be immediately calculated after the flowJo workspace have been imported. TRUE by default.TRUE|FALSE logical specifying if you would like to use netcdf to store the data, or if you would like to keep all the flowFrames in memory. For a small data set, you can safely set this to FALSE, but for larger data, we suggest using netcdf. You will need the netcdf C library installed.numeric vector specifying the subset of samples in a group to import. Or a character specifying the FCS filenames to be imported.logical Should samples that have no gates be included?logical Should gates be imported, or just the data with compensation and transformation?character scalar indicating where to get sampleName(or FCS filename) within xml workspace. It is either from "keyword" or "sampleNode".matrix that allow the customized compensation matrix to be used instead of the one specified in flowJo workspace.
integer option passed to xmlTreeParse
logical flag indicates whether the colnames(channel names) matching needs to be case sensitive (e.g. compensation, gating..)
numeric the threshold that determine wether the gates need to be extended. default is 0. It is triggered when gate coordinates are below this value.
numeric the value that gate coordinates are extended to. Default is -4000. Usually this value will be automatically detected according to the real data range.
But when the gates needs to be extended without loading the raw data (i.e. execute is set to FALSE), then this hard-coded value is used.
GatingSet, which is a wrapper around a list of GatingHierarchy objects, each representing a single sample in the workspace. The GatingHierarchy objects contain graphNEL trees that represent the gating hierarchy of each sample. Each node in the GatingHierarchy has associated data, including the population counts from flowJo, the parent population counts, the flowCore gates generated from the flowJo workspace gate definitions. Data are not yet loaded or acted upon at this stage. To execute the gating of each data file, a call to execute() must be made on each GatingHierarchy object in the GatingSet. This is done automatically by default, and there is no more reason to set this argument to FALSE.
openWorkspace(), passing the name of the xml workspace file. This returns a flowJoWorkspace, which can be parsed using the parseWorkspace() method. The function can be called non-interactively by passing the index or name of the group of samples to be imported via parseWorkspace(obj,name=x), where x is either the numeric index, or the name.
The subset argument allows one to select a set of files from the chosen sample group. The routine will take the intersection of the files in the sample group, the files specified in subset and the files available on disk, and import them.
getSampleGroups,GatingSet
## Not run:
# #f is a xml file name of a flowJo workspace
# ws<-openWorkspace(f)
# G<-parseWorkspace(ws,execute=TRUE,isNcdf=FALSE,path="."); #assume that the fcs files are below the current directory.
# #G is a GatingSet.
# G1<-parseWorkspace(ws)
# #G1 is a GatingSet.
# ## End(Not run)
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