GatingML interface for openCyto

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Documentation for package ‘CytoML’ version 1.0.1

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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