flowWorkspace: Infrastructure for representing and interacting with the gated cytometry

This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.

AuthorGreg Finak, Mike Jiang
Date of publicationNone
MaintainerGreg Finak <gfinak@fhcrc.org>,Mike Jiang <wjiang2@fhcrc.org>
LicenseArtistic-2.0
Version3.20.3

View on Bioconductor

Man pages

add: Create a GatingSet and add/remove the flowCore gate(or...

asinh_Gml2: inverse hyperbolic sine transform function generator...

asinhtGml2_trans: Inverse hyperbolic sine transformation.

booleanFilter-class: A class describing logical operation (& or |) of the...

checkRedundantNodes: try to determine the redundant terminal(or leaf) nodes that...

clone: clone a GatingSet

compensate: compensate the flow data asssociated with the GatingSet

dropRedundantChannels: Remove the channels from flow data that are not used by gates

dropRedundantNodes: Remove the terminal leaf nodes that make the gating trees to...

estimateLogicle.GatingHierarchy: Compute logicle transformation from the flowData associated...

filterObject: convert flowCore filter to a list It convert the flowCore...

flow_breaks: Generate the breaks that makes sense for flow data...

flowData: Fetch or replace the flowData object associated with a...

flowJo_biexp_trans: flowJo biexponential transformation.

flowJo.fasinh: inverse hyperbolic sine transform function

flowJo_fasinh_trans: flowJo inverse hyperbolic sine transformation.

flowJoTrans: construct the flowJo-type biexponentioal transformation...

flowJoWorkspace-class: An R representation of a flowJo workspace.

flow_trans: helper function to generate a trans objects Used by other...

flowWorkspace-package: Import and replicate flowJo workspaces and gating schemes...

flowWorkspace.par.get: flowWorkspace.par.set sets a set of parameters in the...

flowWorkspace.par.init: workspace version is parsed from xml node...

GatingHierarchy-class: Class GatingHierarchy

GatingSet-class: Class '"GatingSet"'

GatingSetList-class: Class '"GatingSetList"'

GatingSet-methods: constructors for GatingSet

getCompensationMatrices: Retrieve the compensation matrices from a GatingHierarchy

getData-methods: get gated flow data from a...

getFJWSubsetIndices: Fetch the indices for a subset of samples in a flowJo...

getGate: Return the flowCore gate definition associated with a node in...

getIndiceMat: Return the single-cell matrix of 1/0 dichotomized expression

getIndices: Get the membership indices for each event with respect to a...

getIndices-GatingSet-name-method: routine to return the indices by specify boolean combination...

getKeywords: Get Keywords

getNodes: Get the names of all nodes from a gating hierarchy.

getParent: Return the name of the parent population or a list of child...

getPopStats: Return a table of population statistics for all populations...

getSampleGroups: Get a table of sample groups from a flowJo workspace

getSamples: Get a list of samples from a flowJo workspace

getSingleCellExpression: Return the cell events data that express in any of the single...

getTransformations: Return a list of transformations or a transformation in a...

groupByChannels: split GatingSets into groups based on their flow channels

groupByTree: split GatingSets into groups based on their gating schemes Be...

insertGate: insert a dummy gate to the GatingSet

isNcdf: determine the flow data associated with a Gating Hiearchy is...

keyword: Retrieve a specific keyword for a specific sample in a...

lapply-methods: apply 'FUN' to each sample (i.e. 'GatingHierarchy')

length: Methods to get the length of a GatingSet

logicleGml2_trans: GatingML2 version of logicle transformation.

logicle_trans: logicle transformation.

loglevel: get/set the log level

markernames: Get/set the column(channel) or marker names

mkformula: make a formula from a character vector

ncFlowSet-methods: Fetch the flowData object associated with a GatingSet .

openWorkspace: Open/Close a flowJo workspace

parseWorkspace: Parse a flowJo Workspace

pData-methods: read/set pData of flow data associated with 'GatingSet' or...

plotGate-methods: Plot gates and associated cell population contained in a...

plot-methods: plot a gating tree

plotPopCV: Plot the coefficient of variation between flowJo and flowCore...

prettyAxis: Determine tick mark locations and labels for a given channel...

recompute: Compute the cell events by the gates stored within the gating...

sampleNames: Get/update sample names in a GatingSet

save_gs: save/load a GatingSet/GatingSetList to/from disk.

setGate: update the gate

setNode-methods: Update the name of one node in a gating hierarchy/GatingSet.

standardize-GatingSet: The tools to standardize the tree structures and channel...

subset: subset the GatingSet/GatingSetList based on 'pData'

transform: tranform the flow data asssociated with the GatingSet

transformerList: Constructor for transformerList object

updateChannels: Update the channel information of a GatingSet (c++ part)

Files in this package

flowWorkspace/DESCRIPTION
flowWorkspace/INSTALL
flowWorkspace/NAMESPACE
flowWorkspace/R
flowWorkspace/R/AllClasses.R flowWorkspace/R/AllGenerics.R flowWorkspace/R/GatingHierarchy_Methods.R flowWorkspace/R/GatingSetList_Methods.R flowWorkspace/R/GatingSet_Methods.R flowWorkspace/R/RcppExports.R flowWorkspace/R/add_Methods.R flowWorkspace/R/filterObject_Methods.R flowWorkspace/R/flowJoWorkspace_Methods.R flowWorkspace/R/flow_trans.R flowWorkspace/R/merge_GatingSet.R flowWorkspace/R/setGate_Methods.R flowWorkspace/R/utils.R flowWorkspace/R/zzz.R
flowWorkspace/README.md
flowWorkspace/build
flowWorkspace/build/vignette.rds
flowWorkspace/cleanup
flowWorkspace/configure
flowWorkspace/configure.ac
flowWorkspace/example
flowWorkspace/inst
flowWorkspace/inst/NEWS
flowWorkspace/inst/cppTest
flowWorkspace/inst/cppTest/unitTest
flowWorkspace/inst/cppTest/unitTest/computeCalibrationTable.cpp
flowWorkspace/inst/cppTest/unitTest/cpConstructorTest.cpp
flowWorkspace/inst/cppTest/unitTest/gatingSet_test.cpp
flowWorkspace/inst/cppTest/unitTest/ncdfFlow.cpp
flowWorkspace/inst/cppTest/unitTest/ncdfFlow.hpp
flowWorkspace/inst/cppTest/unitTest/ncdf_test.cpp
flowWorkspace/inst/cppTest/unitTest/spline_test.cpp
flowWorkspace/inst/cppTest/unitTest/src.cpp
flowWorkspace/inst/cppTest/unitTest/testSuite.cpp
flowWorkspace/inst/cppTest/unitTest/test_header.hpp
flowWorkspace/inst/doc
flowWorkspace/inst/doc/HowToMergeGatingSet.R
flowWorkspace/inst/doc/HowToMergeGatingSet.Rmd
flowWorkspace/inst/doc/HowToMergeGatingSet.html
flowWorkspace/inst/doc/plotGate.R
flowWorkspace/inst/doc/plotGate.Rmd
flowWorkspace/inst/doc/plotGate.html
flowWorkspace/inst/extdata
flowWorkspace/inst/extdata/empty_workspace_9.2.xml
flowWorkspace/inst/include
flowWorkspace/inst/include/flowWorkspace
flowWorkspace/inst/include/flowWorkspace.h
flowWorkspace/inst/javascript
flowWorkspace/inst/javascript/showPlot.js
flowWorkspace/inst/tests
flowWorkspace/inst/tests/expect_result
flowWorkspace/man
flowWorkspace/man/GatingHierarchy-class.Rd flowWorkspace/man/GatingSet-class.Rd flowWorkspace/man/GatingSet-methods.Rd flowWorkspace/man/GatingSetList-class.Rd flowWorkspace/man/add.Rd flowWorkspace/man/asinh_Gml2.Rd flowWorkspace/man/asinhtGml2_trans.Rd flowWorkspace/man/booleanFilter-class.Rd flowWorkspace/man/checkRedundantNodes.Rd flowWorkspace/man/clone.Rd flowWorkspace/man/compensate.Rd flowWorkspace/man/dropRedundantChannels.Rd flowWorkspace/man/dropRedundantNodes.Rd flowWorkspace/man/estimateLogicle.GatingHierarchy.Rd flowWorkspace/man/filterObject.Rd flowWorkspace/man/flowData.Rd flowWorkspace/man/flowJo.fasinh.Rd flowWorkspace/man/flowJoTrans.Rd flowWorkspace/man/flowJoWorkspace-class.Rd flowWorkspace/man/flowJo_biexp_trans.Rd flowWorkspace/man/flowJo_fasinh_trans.Rd flowWorkspace/man/flowWorkspace-package.Rd flowWorkspace/man/flowWorkspace.par.get.Rd flowWorkspace/man/flowWorkspace.par.init.Rd flowWorkspace/man/flow_breaks.Rd flowWorkspace/man/flow_trans.Rd flowWorkspace/man/getCompensationMatrices.Rd flowWorkspace/man/getData-methods.Rd flowWorkspace/man/getFJWSubsetIndices.Rd flowWorkspace/man/getGate.Rd flowWorkspace/man/getIndiceMat.Rd flowWorkspace/man/getIndices-GatingSet-name-method.Rd flowWorkspace/man/getIndices.Rd flowWorkspace/man/getKeywords.Rd flowWorkspace/man/getNodes.Rd flowWorkspace/man/getParent.Rd flowWorkspace/man/getPopStats.Rd flowWorkspace/man/getSampleGroups.Rd flowWorkspace/man/getSamples.Rd flowWorkspace/man/getSingleCellExpression.Rd flowWorkspace/man/getTransformations.Rd flowWorkspace/man/groupByChannels.Rd flowWorkspace/man/groupByTree.Rd flowWorkspace/man/insertGate.Rd flowWorkspace/man/isNcdf.Rd flowWorkspace/man/keyword.Rd flowWorkspace/man/lapply-methods.Rd flowWorkspace/man/length.Rd flowWorkspace/man/logicleGml2_trans.Rd flowWorkspace/man/logicle_trans.Rd flowWorkspace/man/loglevel.Rd flowWorkspace/man/markernames.Rd flowWorkspace/man/mkformula.Rd flowWorkspace/man/ncFlowSet-methods.Rd flowWorkspace/man/openWorkspace.Rd flowWorkspace/man/pData-methods.Rd flowWorkspace/man/parseWorkspace.Rd flowWorkspace/man/plot-methods.Rd flowWorkspace/man/plotGate-methods.Rd flowWorkspace/man/plotPopCV.Rd flowWorkspace/man/prettyAxis.Rd flowWorkspace/man/recompute.Rd flowWorkspace/man/sampleNames.Rd flowWorkspace/man/save_gs.Rd flowWorkspace/man/setGate.Rd flowWorkspace/man/setNode-methods.Rd flowWorkspace/man/standardize-GatingSet.Rd flowWorkspace/man/subset.Rd flowWorkspace/man/transform.Rd flowWorkspace/man/transformerList.Rd flowWorkspace/man/updateChannels.Rd
flowWorkspace/src
flowWorkspace/src/GatingHierarchy.cpp
flowWorkspace/src/GatingSet.cpp
flowWorkspace/src/GatingSet.pb.cc
flowWorkspace/src/GatingSet.pb.h
flowWorkspace/src/GatingSet.proto
flowWorkspace/src/GatingSet_pb2.py
flowWorkspace/src/Makevars.in
flowWorkspace/src/Makevars.win
flowWorkspace/src/POPINDICES.cpp
flowWorkspace/src/R_API.cpp
flowWorkspace/src/R_GatingHierarchy.cpp
flowWorkspace/src/R_GatingSet.cpp
flowWorkspace/src/RcppExports.cpp
flowWorkspace/src/boost_serialization
flowWorkspace/src/boost_serialization/boost
flowWorkspace/src/boost_serialization/boost/archive
flowWorkspace/src/boost_serialization/boost/serialization
flowWorkspace/src/calibrationTable.cpp
flowWorkspace/src/compensation.cpp
flowWorkspace/src/delimitedMessage.cpp
flowWorkspace/src/flowData.cpp
flowWorkspace/src/flowJoWorkspace.cpp
flowWorkspace/src/gate.cpp
flowWorkspace/src/global.cpp
flowWorkspace/src/include
flowWorkspace/src/include/GatingHierarchy.hpp
flowWorkspace/src/include/GatingSet.hpp
flowWorkspace/src/include/POPINDICES.hpp
flowWorkspace/src/include/calibrationTable.hpp
flowWorkspace/src/include/compensation.hpp
flowWorkspace/src/include/delimitedMessage.hpp
flowWorkspace/src/include/flowData.hpp
flowWorkspace/src/include/flowJoWorkspace.hpp
flowWorkspace/src/include/gate.hpp
flowWorkspace/src/include/global.hpp
flowWorkspace/src/include/macFlowJoWorkspace.hpp
flowWorkspace/src/include/nodeProperties.hpp
flowWorkspace/src/include/populationTree.hpp
flowWorkspace/src/include/spline.hpp
flowWorkspace/src/include/transformation.hpp
flowWorkspace/src/include/winFlowJoWorkspace.hpp
flowWorkspace/src/include/workspace.hpp
flowWorkspace/src/include/wsNode.hpp
flowWorkspace/src/macFlowJoWorkspace.cpp
flowWorkspace/src/nodeProperties.cpp
flowWorkspace/src/pb_build
flowWorkspace/src/pb_build/Makefile
flowWorkspace/src/pb_build/config.h
flowWorkspace/src/pb_build/config.log
flowWorkspace/src/pb_build/config.status
flowWorkspace/src/pb_build/libtool
flowWorkspace/src/pb_build/protobuf-lite.pc
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flowWorkspace/src/pb_build/src/google
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flowWorkspace/src/pb_build/src/google/protobuf/.libs/extension_set.o
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flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_arm_gcc.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_arm_qnx.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_atomicword_compat.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_generic_gcc.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_macosx.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_mips_gcc.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_pnacl.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_tsan.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_gcc.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_gcc.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_msvc.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/atomicops_internals_x86_msvc.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/common.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/common.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/hash.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/map_util.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/once.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/once.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/platform_macros.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/shared_ptr.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/stl_util.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/stringprintf.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/structurally_valid.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/strutil.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/strutil.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/substitute.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/substitute.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/template_util.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/stubs/type_traits.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/testing
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/testing/file.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/testing/file.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/testing/googletest.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/testing/googletest.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/testing/zcgunzip.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/testing/zcgzip.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/text_format.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/text_format.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/unknown_field_set.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/unknown_field_set.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/wire_format.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/wire_format.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/wire_format_lite.cc
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/wire_format_lite.h
flowWorkspace/src/protobuf-2.6.0/src/google/protobuf/wire_format_lite_inl.h
flowWorkspace/src/protobuf-2.6.0/src/solaris
flowWorkspace/src/protobuf-2.6.0/src/solaris/libstdc++.la
flowWorkspace/src/serialization
flowWorkspace/src/spline.cpp
flowWorkspace/src/transformation.cpp
flowWorkspace/src/unitTest
flowWorkspace/src/winFlowJoWorkspace.cpp
flowWorkspace/src/workspace.cpp
flowWorkspace/src/wsNode.cpp
flowWorkspace/tests
flowWorkspace/tests/testthat
flowWorkspace/tests/testthat.R
flowWorkspace/tests/testthat/GatingHierarchy-testSuite.R
flowWorkspace/tests/testthat/GatingSet-testSuite.R
flowWorkspace/tests/testthat/GatingSetList-testSuite.R
flowWorkspace/tests/testthat/InternalTestSuite.R
flowWorkspace/tests/testthat/expect_result
flowWorkspace/tests/testthat/expect_result/cv_gh.rds
flowWorkspace/tests/testthat/expect_result/cv_gs.csv
flowWorkspace/tests/testthat/expect_result/flowJoWorkspace_expect.rds
flowWorkspace/tests/testthat/expect_result/getAllDescendants_cd3_gh.rds
flowWorkspace/tests/testthat/expect_result/getAllDescendants_cd4_gh.rds
flowWorkspace/tests/testthat/expect_result/getAllDescendants_cd8_gh.rds
flowWorkspace/tests/testthat/expect_result/getAxisLabels_gh.rds
flowWorkspace/tests/testthat/expect_result/getCompensationMatrices_gh.rds
flowWorkspace/tests/testthat/expect_result/getData_COMPASS_gs.rds
flowWorkspace/tests/testthat/expect_result/getGate_gs.rds
flowWorkspace/tests/testthat/expect_result/getGate_gs_ellipse.rds
flowWorkspace/tests/testthat/expect_result/getGate_gs_polygon.rds
flowWorkspace/tests/testthat/expect_result/getGraph_gh.rds
flowWorkspace/tests/testthat/expect_result/getIndiceMat_gh.rds
flowWorkspace/tests/testthat/expect_result/getIndice_singlet_gh.rds
flowWorkspace/tests/testthat/expect_result/getIndices_gs.rds
flowWorkspace/tests/testthat/expect_result/getNodes_gh.rds
flowWorkspace/tests/testthat/expect_result/getPopStats_gh.csv
flowWorkspace/tests/testthat/expect_result/getPopStats_gs.csv
flowWorkspace/tests/testthat/expect_result/getTransformations_gh.rds
flowWorkspace/tests/testthat/expect_result/kw_gh.rds
flowWorkspace/tests/testthat/expect_result/kw_gs.rds
flowWorkspace/tests/testthat/expect_result/layoutGraph_gh.rds
flowWorkspace/tests/testthat/flowJoWorkspace-testSuite.R
flowWorkspace/tests/testthat/helper-expectResult.R
flowWorkspace/tests/testthat/test-archive.R
flowWorkspace/tests/testthat/test-compensate.R
flowWorkspace/tests/testthat/test-filterObject.R
flowWorkspace/tests/testthat/test-merge.R
flowWorkspace/tests/testthat/test-misc.R
flowWorkspace/tests/testthat/test-parseWorkspace.R
flowWorkspace/vignettes
flowWorkspace/vignettes/HowToMergeGatingSet.Rmd
flowWorkspace/vignettes/flowWorkspace-Introduction.Rmd
flowWorkspace/vignettes/plotGate.Rmd

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