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.
HOW TO COMPENSATE IN FLOWJO 10 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 ) flowjo_to_gatingset ( ws, name = NULL, subset = list (), execute = TRUE, path = "", cytoset = NULL, backend_dir = tempdir (), backend = get_default_backend (), includeGates = TRUE, additional.keys = "$TOT", additional.sampleID = FALSE, keywords = character (), keywords.source = "XML", = FALSE, extend_val = 0, extend_to = -4000, = FALSE, leaf.bool = TRUE, include_empty_tree = FALSE, skip_faulty_gate = FALSE, compensation = NULL, transform = TRUE, fcs_file_extension = ".fcs", greedy_match = FALSE, mc.cores = 1. ) # S4 method for signature 'flowjo_workspace' parseWorkspace ( obj.
show-graphGML-method: show method for graphGML. : Parser for gatingML exported by Cytobank. range.GatingHierarchy: the parameter range from the flow data associated with. plot-graphGML-missing-method: plot the population tree stored in graphGML. parse.gateInfo: Parse the cytobank custom_info for each gate. open_flowjo_xml: Open/Close a flowJo workspace. 
open_cytobank_experiment: Construct a 'cytobank_experiment' object from ACS file. matchPath: Given the leaf node, try to find out if a collection of nodes. gs_compare_cytobank_counts: compare the counts to cytobank's exported csv so that the. graphGML-class: A graph object returned by '' function. aphGML: Extract transformations from graphGML object. getParent-graphGML-character-method: get parent nodes. getNodes-graphGML-method: get nodes from graphGML object. getGate-graphGML-character-method: get gate from the node. aphGML: Extract compensation from graphGML object. getChildren-graphGML-character-method: get children nodes. gatingset_to_flowjo: Convert a GatingSet to flowJo workspace. gatingset_to_cytobank: Convert a GatingSet to a Cytobank-compatible gatingML. flowjo_workspace-class: An R representation of a flowJo workspace. flowjo_to_gatingset: Parse a flowJo Workspace. 
fj_ws_get_samples: Get a list of samples from a flowJo workspace. 
fj_ws_get_sample_groups: Get a table of sample groups from a flowJo workspace. extend: extend the gate to the minimum and maximum limit of both. diva_workspace-class: An R representation of a BD FACSDiva workspace. diva_to_gatingset: Parse a FACSDiva Workspace. diva_get_samples: Get a table of samples from a FACSDiva workspace. : workspace version is parsed from xml node. : sets a set of parameters in the CytoML package. CytoML-deprecated: Deprecated functions in package 'CytoML'. cytobank_to_gatingset: A wrapper that parses the gatingML and FCS files (or. cytobank_experiment-methods: Methods for interacting with cytobank_experiment objects. 
constructTree: Reconstruct the population tree from the GateSets. compensate-GatingSet-graphGML-method: compensate a GatingSet based on the compensation information. ce_get_transformations: Obtain the transformations associated with each channel in a. ce_get_samples: Obtain a mapping between the samples and marker panels in a. ce_get_panels: Obtain counts of the number of samples associated with each. ce_get_compensations: Obtain the spillover matrices for the samples in a Cytobank. addCustomInfo: add customInfo nodes to each gate node and add.
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