# A GatingML Interface for Cross Platform Cytometry Data Sharing

## Documentation for package ‘CytoML’ version 2.0.5

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

## Help Pages

addCustomInfo | add customInfo nodes to each gate node and add BooleanAndGates
ce_get_compensations | Obtain the spillover matrices for the samples in a Cytobank experiment
ce_get_panels | Obtain counts of the number of samples associated with each marker panel in a Cytobank experiment
ce_get_samples | Obtain a mapping between the samples and marker panels in a Cytobank experiment
ce_get_transformations | Obtain the transformations associated with each channel in a Cytobank experiment
colnames-method | Methods for interacting with cytobank_experiment objects
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 parses the gatingML and FCS files (or 'cytobank_experiment' object) into GatingSet
cytobankExperiment | Construct a 'cytobank_experiment' object from ACS file
cytobank_experiment-methods | Methods for interacting with cytobank_experiment objects
cytobank_to_gatingset | A wrapper that parses the gatingML and FCS files (or 'cytobank_experiment' object) into GatingSet
cytobank_to_gatingset.cytobank_experiment | A wrapper that parses the gatingML and FCS files (or 'cytobank_experiment' object) into GatingSet
cytobank_to_gatingset.default | A wrapper that parses the gatingML and FCS files (or 'cytobank_experiment' object) into GatingSet
CytoML-deprecated | Deprecated functions in package 'CytoML'.
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 | Get a table of samples from a FACSDiva workspace
diva_get_sample_groups | Get a table of samples from a FACSDiva workspace
diva_to_gatingset | Parse a FACSDiva Workspace
diva_workspace-class | An R representation of a BD FACSDiva workspace
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.
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.
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.
markernames-method | Methods for interacting with cytobank_experiment objects
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 a '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 | Parse a flowJo Workspace
parseWorkspace-method | Parse a FACSDiva Workspace
parseWorkspace-method | Parse a flowJo Workspace
pData-method | Methods for interacting with cytobank_experiment objects
plot-method | plot the population tree stored in graphGML.
print.cytobank_experiment | Methods for interacting with cytobank_experiment objects
range.GatingHierarchy | the parameter range from the flow data associated with GatingHierarchy
read.gatingML.cytobank | Parser for gatingML exported by Cytobank
sampleNames-method | Methods for interacting with cytobank_experiment objects
show-method | An R representation of a BD FACSDiva workspace
show-method | An R representation of a flowJo workspace.
show-method | show method for graphGML