openCyto: Hierarchical Gating Pipeline for flow cytometry data

This package is designed to facilitate the automated gating methods in sequential way to mimic the manual gating strategy.

Install the latest version of this package by entering the following in R:
source("https://bioconductor.org/biocLite.R")
biocLite("openCyto")
AuthorMike Jiang, John Ramey, Greg Finak, Raphael Gottardo
Bioconductor views DataImport DataRepresentation FlowCytometry Preprocessing
Date of publicationNone
MaintainerMike Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version1.14.0

View on Bioconductor

Man pages

add: bypass the default flowWorkspace:::.addGate

add_pop: apply a gating method to the 'GatingSet'

as.data.table.gatingTemplate: convert a gatingTemplate object to a data.table

boolMethod-class: A class to represent a boolean gating method.

dims-gtMethod-method: get gating method dimensions

dummyMethod-class: A class to represent a dummy gating method that does nothing...

fcEllipsoidGate: constuctor for 'fcEllipsoidGate'

fcEllipsoidGate-class: a concrete class that reprents the ellipsoidGate generated by...

fcFilter-class: a virtual class that represents the gating result generated...

fcFilterList: constuctor for 'fcFilterList'

fcFilterList-class: a class that extends 'filterList' class.

fcPolygonGate: constuctor for 'fcPolygonGate'

fcPolygonGate-class: a concrete class that reprents the polygonGate generated by...

fcRectangleGate: constuctor for 'fcRectangleGate'

fcRectangleGate-class: a concrete class that reprents the rectangleGate generated by...

fcTree: constructor of 'fcTree'

fcTree-class: A class to represent a flowClust tree.

filterObject-logicalFilterResult-method: construct logicalGate obj

flowClust1d: Applies flowClust to 1 feature to determine a cutpoint...

flowClust2d: Automatic identification of a population of interest via...

gate_mindensity: Determines a cutpoint as the minimum point of a kernel...

gate_mindensity2: An improved version of mindensity used to determines a...

gate_quad_sequential: sequential quadrant gating function

gate_quad_tmix: quadGate based on flowClust::tmixFiler

gate_quantile: Determine the cutpoint by the events quantile.

gate_tail: Gates the tail of a density using the derivative of a kernel...

gating-gtMethod-GatingSet-method: apply a gtMethod to the 'GatingSet'

gating-methods: Apply the gates to a GatingSet

gatingTemplate-class: a class storing the gating method and population information...

getChildren-gatingTemplate-character-method: get children nodes

getGate-fcTree-character-method: get gates saved in 'fcTree'

getGate-gatingTemplate-character-method: get gating method from the node

getNodes: get nodes from gatingTemplate object

getNodes-fcTree-method: get nodes from 'fcTree'

getParent-gatingTemplate-character-method: get parent nodes

groupBy-gtMethod-method: get the grouping variable for the gating method

gtMethod-class: A class to represent a gating method.

gtPopulation-class: A class to represent a cell population that will be generated...

gtSubsets-class: A class representing a group of cell populations.

isCollapse-gtMethod-method: get the flag that determines whether gating method is applied...

isPolyfunctional: A function to tell wether a gating method is 'polyFunctions'

listgtMethods: Print a list of the registered gating methods

names-gtMethod-method: get gating method name

names-gtPopulation-method: get population name

ocRectangleGate-class: the class that carries event indices as well

ocRectRefGate: constructor for ocRectRefGate

ocRectRefGate-class: special gate type that mix the rectangleGate with boolean...

openCyto: Hierarchical Gating Pipeline for flow cytometry data

parameters-gtMethod-method: get parameters of the gating method/function

plot-fcFilterList-ANY-method: plot a 'fcFilterList'

plot-fcTree-character-method: plot the flowClust gating results

plot-gatingTemplate-missing-method: plot the gating scheme

polyFunctions-class: A class to represent a polyFunctions gating method.

posteriors-fcFilter-ANY-method: get posteriors from a 'fcFilter' object

ppMethod-class: A class to represent a preprocessing method.

ppMethod-gatingTemplate-character-method: get preprocessing method from the node

preprocessing-ppMethod-GatingSet-method: apply a ppMethod to the 'GatingSet'

prior_flowClust: Elicits data-driven priors from a flowSet object for...

prior_flowClust1d: Elicits data-driven priors from a flowSet object for a...

prior_kmeans: Elicits data-driven priors from a flowSet object for...

priors-fcFilter-ANY-method: get priors from a 'fcFilter' object

refGate-class: A class to represent a reference gating method.

registerPlugins: Register a gating or preprocessing function with OpenCyto

show-boolMethod-method: show method for boolMethod

show-fcFilter-method: show method for fcFilter

show-gatingTemplate-method: show method for gatingTemplate

show-gtMethod-method: show method for gtMethod

templateGen: generate a partially complete csv template from the existing...

toggle.helperGates: toggle/delete the hidden flag of the helper gates

Functions

add,GatingHierarchy,logicalFilterResult-method Man page
add,GatingHierarchy,multipleFilterResult-method Man page
add,GatingHierarchy,ocRectangleGate-method Man page
add,GatingHierarchy,ocRectRefGate-method Man page
add_pop Man page
as.data.table.gatingTemplate Man page
boolMethod-class Man page
cytokine Man page
delete.helperGates Man page
dims,gtMethod-method Man page
dummyMethod-class Man page
fcEllipsoidGate Man page
fcEllipsoidGate-class Man page
fcFilter-class Man page
fcFilterList Man page
fcFilterList-class Man page
fcPolygonGate Man page
fcPolygonGate-class Man page
fcRectangleGate Man page
fcRectangleGate-class Man page
fcTree Man page
fcTree-class Man page
filterObject,logicalFilterResult-method Man page
flowClust.1d Man page
flowClust.2d Man page
gate_flowClust_1d Man page
gate_flowClust_2d Man page
gate_mindensity Man page
gate_mindensity2 Man page
gate_quad_sequential Man page
gate_quad_tmix Man page
gate_quantile Man page
gate_tail Man page
gating Man page
gating,boolMethod,GatingSetList-method Man page
gating,boolMethod,GatingSet-method Man page
gating,dummyMethod,GatingSetList-method Man page
gating,dummyMethod,GatingSet-method Man page
gating,gatingTemplate,GatingSetList-method Man page
gating,gatingTemplate,GatingSet-method Man page
gating,gtMethod,GatingSetList-method Man page
gating,gtMethod,GatingSet-method Man page
gating,polyFunctions,GatingSetList-method Man page
gating,polyFunctions,GatingSet-method Man page
gating,refGate,GatingSetList-method Man page
gating,refGate,GatingSet-method Man page
gatingTemplate Man page
gatingTemplate,character-method Man page
gatingTemplate-class Man page
getChildren,gatingTemplate,character-method Man page
getGate,fcTree,character-method Man page
getGate,gatingTemplate,character-method Man page
get.helperGates Man page
getNodes,fcTree-method Man page
getNodes,gatingTemplate-method Man page
getParent,gatingTemplate,character-method Man page
groupBy,gtMethod-method Man page
gtMethod-class Man page
gtPopulation-class Man page
gtSubsets-class Man page
isCollapse,gtMethod-method Man page
.isPolyfunctional Man page
listgtMethods Man page
mindensity Man page
mindensity2 Man page
names,gtMethod-method Man page
names,gtPopulation-method Man page
ocRectangleGate-class Man page
ocRectRefGate Man page
ocRectRefGate-class Man page
openCyto Man page
openCyto-package Man page
parameters,gtMethod-method Man page
plot,fcFilterList,ANY-method Man page
plot,fcTree,character-method Man page
plot,gatingTemplate,ANY-method Man page
plot,gatingTemplate,character-method Man page
plot,gatingTemplate-method Man page
plot,gatingTemplate,missing-method Man page
polyFunctions-class Man page
posteriors,fcFilter,ANY-method Man page
posteriors,fcFilter,character-method Man page
ppMethod-class Man page
ppMethod,gatingTemplate,character-method Man page
preprocessing,ppMethod,GatingSet-method Man page
prior_flowClust Man page
.prior_flowClust1d Man page
.prior_kmeans Man page
priors,fcFilter,ANY-method Man page
priors,fcFilter,character-method Man page
quadGate.seq Man page
quadGate.tmix Man page
quantileGate Man page
refGate-class Man page
registerGatingFunction Man page
registerPlugins Man page
show,boolMethod-method Man page
show,fcFilter-method Man page
show,gatingTemplate-method Man page
show,gtMethod-method Man page
tailgate Man page
templateGen Man page
toggle.helperGates Man page

Files

DESCRIPTION
NAMESPACE
R
R/AllClasses.R R/RcppExports.R R/add.R R/add_pop.R R/as.data.table.R R/bayes-flowClust.R R/coerce.R R/csvTemplate-parser.R R/fcFilter-methods.R R/fcFilterList-methods.R R/fcTree-methods.R R/functions.R R/gating-functions.R R/gating-methods.R R/gatingTemplate-methods.R R/gtMethod-methods.R R/gtPopulation-methods.R R/mindensity2.R R/pluginFramework.R R/preprocessing-method.R R/toggle.helperGates.R R/unlockNamespace.R R/wrapper-functions.R R/zzz.R
README.md
build
build/vignette.rds
example
inst
inst/CITATION
inst/NEWS
inst/doc
inst/doc/HowToAutoGating.R
inst/doc/HowToAutoGating.Rmd
inst/doc/HowToAutoGating.html
inst/doc/HowToWriteCSVTemplate.R
inst/doc/HowToWriteCSVTemplate.Rmd
inst/doc/HowToWriteCSVTemplate.html
inst/doc/openCytoVignette.R
inst/doc/openCytoVignette.Rmd
inst/doc/openCytoVignette.html
inst/extdata
inst/extdata/gating_template
inst/extdata/gating_template/ICS.csv
inst/extdata/gating_template/ICS_080.csv
inst/extdata/gating_template/ITN_Newell.csv
inst/extdata/gating_template/bcell.csv
inst/extdata/gating_template/tcell.csv
inst/extdata/gating_template/treg.csv
inst/tests
man
man/add.Rd man/add_pop.Rd man/as.data.table.gatingTemplate.Rd man/boolMethod-class.Rd man/dims-gtMethod-method.Rd man/dummyMethod-class.Rd man/fcEllipsoidGate-class.Rd man/fcEllipsoidGate.Rd man/fcFilter-class.Rd man/fcFilterList-class.Rd man/fcFilterList.Rd man/fcPolygonGate-class.Rd man/fcPolygonGate.Rd man/fcRectangleGate-class.Rd man/fcRectangleGate.Rd man/fcTree-class.Rd man/fcTree.Rd man/filterObject-logicalFilterResult-method.Rd man/flowClust1d.Rd man/flowClust2d.Rd man/gate_mindensity.Rd man/gate_mindensity2.Rd man/gate_quad_sequential.Rd man/gate_quad_tmix.Rd man/gate_quantile.Rd man/gate_tail.Rd man/gating-gtMethod-GatingSet-method.Rd man/gating-methods.Rd man/gatingTemplate-class.Rd man/getChildren-gatingTemplate-character-method.Rd man/getGate-fcTree-character-method.Rd man/getGate-gatingTemplate-character-method.Rd man/getNodes-fcTree-method.Rd man/getNodes.Rd man/getParent-gatingTemplate-character-method.Rd man/groupBy-gtMethod-method.Rd man/gtMethod-class.Rd man/gtPopulation-class.Rd man/gtSubsets-class.Rd man/isCollapse-gtMethod-method.Rd man/isPolyfunctional.Rd man/listgtMethods.Rd man/names-gtMethod-method.Rd man/names-gtPopulation-method.Rd man/ocRectRefGate-class.Rd man/ocRectRefGate.Rd man/ocRectangleGate-class.Rd man/openCyto.Rd man/parameters-gtMethod-method.Rd man/plot-fcFilterList-ANY-method.Rd man/plot-fcTree-character-method.Rd man/plot-gatingTemplate-missing-method.Rd man/polyFunctions-class.Rd man/posteriors-fcFilter-ANY-method.Rd man/ppMethod-class.Rd man/ppMethod-gatingTemplate-character-method.Rd man/preprocessing-ppMethod-GatingSet-method.Rd man/prior_flowClust.Rd man/prior_flowClust1d.Rd man/prior_kmeans.Rd man/priors-fcFilter-ANY-method.Rd man/refGate-class.Rd man/registerPlugins.Rd man/show-boolMethod-method.Rd man/show-fcFilter-method.Rd man/show-gatingTemplate-method.Rd man/show-gtMethod-method.Rd man/templateGen.Rd man/toggle.helperGates.Rd
src
src/RcppExports.cpp
src/misc.cpp
src/unlockNamespace.c
tests
tests/testthat
tests/testthat.R
tests/testthat/expectResults.rds
tests/testthat/gating-testSuite.R
tests/testthat/gatingResults.rds
tests/testthat/helper-expectRes.R tests/testthat/test-misc.R tests/testthat/test-pluginFramework.R tests/testthat/test-template-parsing.R tests/testthat/test_gating_functions.R
vignettes
vignettes/HowToAutoGating.Rmd
vignettes/HowToAutoGating_files
vignettes/HowToAutoGating_files/figure-html
vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-10-1.png
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vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-8-2.png
vignettes/HowToAutoGating_files/figure-html/unnamed-chunk-9-1.png
vignettes/HowToWriteCSVTemplate.Rmd
vignettes/openCytoVignette.Rmd
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