# A GatingML Interface for Cross Platform Cytometry Data Sharing

## Documentation for package ‘CytoML’ version 1.12.1

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

addCustomInfo | add customInfo nodes to each gate node and add BooleanAndGates
closeWorkspace | Open/Close a flowJo workspace
compensate-method | compensate a GatingSet based on the compensation information stored in graphGML object
constructTree | Reconstruct the population tree from the GateSets
cytobank2GatingSet | A wrapper that parse the gatingML and FCS files (or cytobank_experiment object) into GatingSet
cytobankExperiment | Construct cytobank_experiment object from ACS file
cytobank_to_gatingset | A wrapper that parse the gatingML and FCS files (or cytobank_experiment object) into GatingSet
cytobank_to_gatingset.cytobank_experiment | A wrapper that parse the gatingML and FCS files (or cytobank_experiment object) into GatingSet
cytobank_to_gatingset.default | A wrapper that parse the gatingML and FCS files (or cytobank_experiment object) into GatingSet
CytoML.par.get | CytoML.par.set sets a set of parameters in the CytoML package namespace.
CytoML.par.init | workspace version is parsed from xml node '/Workspace/version' in flowJo workspace and matched with this list to dispatch to the one of the three workspace parsers
CytoML.par.set | CytoML.par.set sets a set of parameters in the CytoML package namespace.
diva_get_samples | diva_workspace class Inherited from flowjo_workspace-class
diva_get_sample_groups | diva_workspace class Inherited from flowjo_workspace-class
diva_to_gatingset | diva_workspace class Inherited from flowjo_workspace-class
diva_workspace-class | diva_workspace class Inherited from flowjo_workspace-class
extend | extend the gate to the minimum and maximum limit of both dimensions based on the bounding information.
extend.ellipsoidGate | extend the gate to the minimum and maximum limit of both dimensions based on the bounding information.
extend.polygonGate | extend the gate to the minimum and maximum limit of both dimensions based on the bounding information.
extend.rectangleGate | extend the gate to the minimum and maximum limit of both dimensions based on the bounding information.
fj_ws_get_keywords | Get Keywords
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
flowjo_to_gatingset | Parse a flowJo Workspace
flowjo_workspace-class | An R representation of a flowJo workspace.
flowjo_ws_close | Open/Close a flowJo workspace
gating-method | Apply the gatingML graph to a GatingSet
GatingSet | constructors for GatingSet
GatingSet-method | constructors for GatingSet
GatingSet2cytobank | Convert a GatingSet to a Cytobank-compatible gatingML
GatingSet2flowJo | Convert a GatingSet to flowJo workspace
gatingset_to_cytobank | Convert a GatingSet to a Cytobank-compatible gatingML
gatingset_to_flowjo | Convert a GatingSet to flowJo workspace
getChildren-method | get children nodes
getCompensationMatrices.graphGML | Extract compensation from graphGML object.
getFJWSubsetIndices | Fetch the indices for a subset of samples in a flowJo workspace, based on a keyword value pair
getGate-method | get gate from the node
getKeywords | Get Keywords
getNodes-method | get nodes from graphGML object
getParent-method | get parent nodes
getSampleGroups | Get a table of sample groups from a flowJo workspace
getSamples | Get a list of samples from a flowJo workspace
getTransformations.graphGML | Extract transformations from graphGML object.
graphGML-class | A graph object returned by 'read.gatingML.cytobank' function.
gs_compare_cytobank_counts | compare the counts to cytobank's exported csv so that the parsing result can be verified.
matchPath | Given the leaf node, try to find out if a collection of nodes can be matched to a path in a graph(tree) by the bottom-up searching
openDiva | open Diva xml workspace
open_cytobank_experiment | Construct cytobank_experiment object from ACS file
open_diva_xml | open Diva xml workspace
open_flowjo_xml | Open/Close a flowJo workspace
parse.gateInfo | Parse the cytobank custom_info for each gate
parseWorkspace-method | diva_workspace class Inherited from flowjo_workspace-class
parseWorkspace-method | Parse a flowJo Workspace
plot-method | plot the population tree stored in graphGML.
range.GatingHierarchy | the parameter range from the flow data associated with GatingHierarchy
read.gatingML.cytobank | Parser for gatingML exported by Cytobank
show-method | diva_workspace class Inherited from flowjo_workspace-class
show-method | An R representation of a flowJo workspace.
show-method | show method for graphGML