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 |
divaWorkspace-class | divaWorkspace class Inherited from flowJoWorkspace-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. |
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 |
getSampleGroups-method | divaWorkspace class Inherited from flowJoWorkspace-class |
getSamples-method | divaWorkspace class Inherited from flowJoWorkspace-class |
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 |
openDiva | open Diva xml workspace |
parse.gateInfo | Parse the cytobank custom_info for each gate |
parseWorkspace-method | divaWorkspace class Inherited from flowJoWorkspace-class |
plot-method | plot the population tree stored in graphGML. |
read.gatingML.cytobank | Parser for gatingML exported by Cytobank |
set.count.xml | save the event counts parsed from xml into c++ tree structure |
show-method | divaWorkspace class Inherited from flowJoWorkspace-class |
show-method | show method for graphGML |