# GatingML interface for openCyto

## Documentation for package ‘CytoML’ version 1.0.1

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

## Help Pages

addCustomInfo | add customInfo nodes to each gate node and add BooleanAndGates
compare.counts | compare the counts to cytobank's exported csv so that the parsing result can be verified.
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 into GatingSet
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.
gating-method | Apply the gatingML graph to a GatingSet
GatingSet2cytobank | Convert a GatingSet to a Cytobank-compatible gatingML
GatingSet2flowJo | Convert a GatingSet to flowJo workspace
getChildren-method | get children nodes
getCompensationMatrices-method | Extract compensation from graphGML object.
getGate-method | get gate from the node
getNodes-method | get nodes from graphGML object
getParent-method | get parent nodes
getTransformations-method | Extract transformations from graphGML object.
graphGML-class | A graph object returned by 'read.gatingML.cytobank' function.
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
parse.gateInfo | Parse the cytobank custom_info for each gate
plot-method | plot the population tree stored in graphGML.
read.gatingML.cytobank | Parser for gatingML exported by Cytobank
show-method | show method for graphGML