CytoML: GatingML interface for openCyto
Version 1.2.0

This package is designed to use GatingML2.0 as the standard format to exchange the gated data with other software platform.

AuthorMike Jiang
Bioconductor views DataImport DataRepresentation FlowCytometry
Date of publicationNone
MaintainerMike Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version1.2.0
Package repositoryView on Bioconductor
InstallationInstall the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("CytoML")

Getting started

README.md
How to export a GatingSet to GatingML
How to parse gatingML into a GatingSet

Popular man pages

constructTree: Reconstruct the population tree from the GateSets
gating-methods: Apply the gatingML graph to a GatingSet
GatingSet2cytobank: Convert a GatingSet to a Cytobank-compatible gatingML
GatingSet2flowJo: Convert a GatingSet to flowJo workspace
getGate-graphGML-character-method: get gate from the node
plot-graphGML-missing-method: plot the population tree stored in graphGML.
read.gatingML.cytobank: Parser for gatingML exported by Cytobank
See all...

All man pages Function index File listing

Man pages

addCustomInfo: add customInfo nodes to each gate node and add...
compare.counts: compare the counts to cytobank's exported csv so that the...
compensate-GatingSet-graphGML-method: compensate a GatingSet based on the compensation information...
constructTree: Reconstruct the population tree from the GateSets
cytobank2GatingSet: A wrapper that parse the gatingML and FCS files into...
divaWorkspace-class: divaWorkspace class Inherited from flowJoWorkspace-class
extend: extend the gate to the minimum and maximum limit of both...
gating-methods: Apply the gatingML graph to a GatingSet
GatingSet2cytobank: Convert a GatingSet to a Cytobank-compatible gatingML
GatingSet2flowJo: Convert a GatingSet to flowJo workspace
getChildren-graphGML-character-method: get children nodes
getCompensationMatrices-graphGML-method: Extract compensation from graphGML object.
getGate-graphGML-character-method: get gate from the node
getNodes-graphGML-method: get nodes from graphGML object
getParent-graphGML-character-method: get parent nodes
getTransformations-graphGML-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...
openDiva: open Diva xml workspace
parse.gateInfo: Parse the cytobank custom_info for each gate
plot-graphGML-missing-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-graphGML-method: show method for graphGML

Functions

GateSetNode Source code
GatingSet2cytobank Man page Source code
GatingSet2flowJo Man page Source code
SampleListNode Source code
addCustomInfo Man page Source code
addExperimentInfo Source code
addGate Source code
addGateSets Source code
base64decode_cytobank Source code
base64encode_cytobank Source code
boolXmlNode Source code
booleanNode Source code
compare.counts Man page Source code
compensate,GatingSet,graphGML-method Man page
constructTree Man page Source code
customInfoNodeForGate Source code
cytobank2GatingSet Man page Source code
datasetNode Source code
divaWorkspace-class Man page
export_comp_trans Source code
export_gates_cytobank Source code
extend Man page Source code
extend.ellipsoidGate Man page Source code
extend.polygonGate Man page Source code
extend.rectangleGate Man page Source code
extend.rectangleGate1d Source code
findParent Source code
fix.ellipsoidGate Source code
fix.rectangleGate Source code
fixChnlName Source code
fjSettings Source code
gateAttr Source code
gateNode Source code
gateNode.default Source code
gateNode.ellipsoidGate Source code
gateNode.polygonGate Source code
gateNode.rectangleGate Source code
gating,graphGML,GatingSet-method Man page
gating.graphGML Source code
getChildren,graphGML,character-method Man page
getCompensationMatrices,graphGML-method Man page
getCustomNodeInfo Source code
getGate,graphGML,character-method Man page
getNodes,graphGML-method Man page
getParent,graphGML,character-method Man page
getPath Source code
getSampleGroups,divaWorkspace-method Man page
getSampleGroupsDiva Source code
getSamples,divaWorkspace-method Man page
getSpilloverMat Source code
getTransformations,graphGML-method Man page
graphGML-class Man page
graphNode Source code
groupNode Source code
inverse Source code
inverse.ellipsoidGate Source code
inverse.polygon Source code
inverse.polygonGate Source code
inverse.rectangleGate Source code
inverseTransGate Source code
is.cytof Source code
keywordNode Source code
matchPath Man page Source code
openDiva Man page Source code
paramerterNode Source code
parse.gateInfo Man page Source code
parseDivaWorkspace Source code
parseWorkspace,divaWorkspace-method Man page
plot,graphGML,missing-method Man page
preprocessorDiva Source code
processGate Source code
read.gatingML.cytobank Man page Source code
sampleNode Source code
set.count.xml Man page Source code Source code
show,divaWorkspace-method Man page
show,graphGML-method Man page
spilloverMatrixNode Source code
spilloverNodes Source code
subPopulationNode Source code
targs Source code
transform.ellipsoidGate Source code
transform.polygonGate Source code
transform.rectangleGate Source code
transformationNode Source code
workspaceNode Source code
xmlDimensionNode Source code
xmlTag Source code
xmlVertexNode Source code

Files

DESCRIPTION
NAMESPACE
R
R/GatingSet2cytobank.R
R/GatingSet2flowJo.R
R/RcppExports.R
R/cytobank2GatingSet.R
R/diva2GatingSet.R
R/flowUtils_functions.R
R/graphGML_methods.R
R/read.gatingML.cytobank.R
R/set.count.xml.R
R/utils.R
README.md
build
build/vignette.rds
configure
configure.ac
inst
inst/NEWS
inst/doc
inst/doc/HowToExportGatingSet.R
inst/doc/HowToExportGatingSet.Rmd
inst/doc/HowToExportGatingSet.html
inst/doc/HowToParseGatingML.R
inst/doc/HowToParseGatingML.Rmd
inst/doc/HowToParseGatingML.html
inst/extdata
inst/extdata/cytotrol_tcell_cytobank.xml
inst/extdata/cytotrol_tcell_cytobank_counts.csv
inst/extdata/diva
inst/extdata/winlist.wlx
inst/tests
man
man/GatingSet2cytobank.Rd
man/GatingSet2flowJo.Rd
man/addCustomInfo.Rd
man/compare.counts.Rd
man/compensate-GatingSet-graphGML-method.Rd
man/constructTree.Rd
man/cytobank2GatingSet.Rd
man/divaWorkspace-class.Rd
man/extend.Rd
man/gating-methods.Rd
man/getChildren-graphGML-character-method.Rd
man/getCompensationMatrices-graphGML-method.Rd
man/getGate-graphGML-character-method.Rd
man/getNodes-graphGML-method.Rd
man/getParent-graphGML-character-method.Rd
man/getTransformations-graphGML-method.Rd
man/graphGML-class.Rd
man/matchPath.Rd
man/openDiva.Rd
man/parse.gateInfo.Rd
man/plot-graphGML-missing-method.Rd
man/read.gatingML.cytobank.Rd
man/set.count.xml.Rd
man/show-graphGML-method.Rd
src
src/CytoML_types.h
src/Makevars
src/Makevars.in
src/Makevars.win
src/RcppExports.cpp
src/setCounts.cpp
tests
tests/testthat
tests/testthat.R
tests/testthat/Cytobank2GatingSet-InternalTestSuite.R
tests/testthat/GatingSet2flowJo-InternalTestSuite.R
tests/testthat/helper-lib.R
tests/testthat/test-cytobank.R
tests/testthat/test-diva2gs.R
tests/testthat/test-extend.R
tests/testthat/test-flowJo.R
vignettes
vignettes/HowToExportGatingSet.Rmd
vignettes/HowToParseGatingML.Rmd
vignettes/cytobank.png
vignettes/flowJo.png
CytoML documentation built on May 20, 2017, 10:34 p.m.

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