#Flowjo reference code

Logical: By default, if flowjo_to_gatingset finds multiple FCS files matching a sample by total event count as well as sampleID and/or keywords specified by additional.keys and additional.sampleID, it will return an error listing the duplicate files. It is mainly for debug purpose (when the raw gates need to be parsed. Logical to enable/disable transformation of gates and data. When some of the samples don't have the external compensations matched, it will fall back to the flowJo xml or FCS looking for the compensation matrix. See 'additional.keys' arguments for details of guids) When it is a list, its names is supposed to be matched to sample guids (Default is the fcs filename suffixed by $TOT. If needed, they can be calculated by calling recompute method at later stage.Ī logical whether to include samples that don't have gates.Ī logical whether to skip the faulty gates so that the parser can still process the rest of gating tree.Ī compensation object, matrix or ame or a list of these objects that allow the customized compensation () to be used instead of the one specified in flowJo workspace or FCS file. COMPASS package will calculate them by itself.) It helps to speed up parsing by turning it off when the statistics of these leaf boolean gates are not important for analysis. compensation, gating.)Ī logical whether to compute the leaf boolean gates. execute is set to FALSE), then this hard-coded value is used.Ī logical flag indicates whether the colnames(channel names) matching needs to be case sensitive (e.g. Usually this value will be automatically detected according to the real data range.īut when the gates needs to be extended without loading the raw data (i.e. Numeric the value that gate coordinates are extended to. It is triggered when gate coordinates are below this value. Numeric the threshold that determine wether the gates need to be extended. Default is FALSE.Ĭharacter vector specifying the keywords to be extracted as pData of GatingSetĬharacter the place where the keywords are extracted from, can be either 'XML' or 'FCS'Ī logical flag indicates whether the keywords matching needs to be case sensitive. This can be helpful when theįilename or other keywords are not enough to differentiate between samples. Default is '$TOT' (total number of cells) and more keywords can be added to make this GUID.īoolean: A boolean specifying whether to include the flowJo sample ID in a GUID to uniquely identify samples. Logical Should gates be imported, or just the data with compensation and transformation?Ĭharacter vector: The keywords (parsed from FCS header) to be combined(concatenated with '_') with FCS filename When cytoset is provided, path argument is ignored. standardize channels using cytoqc package) and then directly use them for flowJo parsing. It is useful sometime to preprocess the raw fcs files When such mapping is provided, the file system searching is avoided.Ī cytoset object that provides the alternative data source other than FCS files. When it is a ame, it is expected to contain two columns:'sampleID' and 'file', which is used as the mapping between 'sampleID' and FCS file (absolute) path.

#Flowjo reference code

The code will search recursively, so you can point it to a location above the files. When character, it is a path to the fcs files that are to be imported. TRUE by default.Įither a character scalar or ame. TRUE|FALSE a logical specifying if the gates, transformations, and compensation should be immediately calculated after the flowJo workspace have been imported. Or an expression to be passed to 'subset' function to filter samples by 'pData' (Note that the columns referred by the expression must also be explicitly specified in 'keywords' argument) Or a character specifying the FCS filenames to be imported. Numeric vector specifying the subset of samples in a group to import. Usually, multiple groups are defined in the flowJo workspace file. If NULL, the groups are printed to the screen and one can be selected interactively. The name or index of the group of samples to be imported. )Īdditional arguments to be passed to FCS parser # S4 method for flowjo_workspace parseWorkspace( obj. The data are not loaded or acted upon until an explicit call to recompute() is made on the GatingHierarchy objects in the GatingSet. Function to parse a flowJo Workspace, generate a GatingHierarchy or GatingSet object, and associated flowCore gates.