# Infrastructure for representing and interacting with gated and ungated cytometry data sets.

## Documentation for package ‘flowWorkspace’ version 4.2.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.

## Help Pages

A B C D E F G I K L M N O P R S T U misc

flowWorkspace-package | Import and replicate flowJo workspaces and gating schemes using flowCore.

## -- A --

add | Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
add-method | Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
asinhtGml2_trans | Inverse hyperbolic sine transformation.
asinh_Gml2 | inverse hyperbolic sine transform function generator (GatingML 2.0 version)

## -- B --

booleanFilter | A class describing logical operation (& or |) of the reference populations
booleanFilter-class | A class describing logical operation (& or |) of the reference populations
brackets | Bracket operators on 'GatingSet' and 'GatingSetList' objects

## -- C --

cf_append_cols | Append data columns to a flowFrame
cf_backend_type | return the cytoframe backend storage format
cf_cleanup | Remove on-disk files associatated with flowWorkspace data classes
cf_cleanup_temp | Remove temporary files associatated with flowWorkspace data classes
cf_flush_meta | Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
cf_get_h5_file_path | Return the file path of the underlying h5 file
cf_get_uri | Return the file path of the underlying h5 file
cf_is_subsetted | check whether a cytoframe/cytoset is a subsetted(by column or by row) view
cf_keyword_delete | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cf_keyword_insert | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cf_keyword_rename | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cf_keyword_set | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cf_load_meta | Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
cf_lock | Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
cf_rename_channel | Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects
cf_rename_marker | Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects
cf_swap_colnames | Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects
cf_unlock | Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
cf_write_disk | Save the cytoframe to disk
cf_write_h5 | Save the cytoframe as h5 format
cf_write_tile | Save the cytoframe as h5 format
char2booleanFilter | A class describing logical operation (& or |) of the reference populations
checkRedundantNodes | try to determine the redundant terminal(or leaf) nodes that can be removed
cleanup | Remove on-disk files associatated with flowWorkspace data classes
cleanup_temp | Remove temporary files associatated with flowWorkspace data classes
colnames-method | Get/set the column(channel) or marker names
colnames<--method | Get/set the column(channel) or marker names
compensate | compensate the flow data asssociated with the GatingSet
compensate-method | compensate the flow data asssociated with the GatingSet
convert | Methods for conversion between flowCore and flowWorkspace data classes
convert_backend | convert h5 based gs archive to tiledb
convert_legacy_gs | convert the legacy GatingSet archive (mixed with R and C++ files) to the new format (C++ only)
convert_legacy_gslist | convert the legacy GatingSet archive (mixed with R and C++ files) to the new format (C++ only)
copyNode | Copy a node along with all of its descendant nodes to the given ancestor
cs_add_cytoframe | Add a cytoframe to a cytoset
cs_cleanup | Remove on-disk files associatated with flowWorkspace data classes
cs_cleanup_temp | Remove temporary files associatated with flowWorkspace data classes
cs_flush_meta | Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
cs_get_cytoframe | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
cs_get_h5_file_path | Return the path of the underlying data files
cs_get_uri | Return the path of the underlying data files
cs_is_subsetted | check whether a cytoframe/cytoset is a subsetted(by column or by row) view
cs_keyword_delete | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cs_keyword_insert | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cs_keyword_rename | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cs_keyword_set | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
cs_load_meta | Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
cs_lock | Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
cs_set_cytoframe | update a cytoframe in a cytoset
cs_swap_colnames | Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects
cs_unlock | Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
cytoframe | 'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
cytoframe-class | 'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
cytoframe-labels | Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects
cytoframe_to_flowFrame | Methods for conversion between flowCore and flowWorkspace data classes
cytoset | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
cytoset-class | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
cytoset_to_flowSet | Methods for conversion between flowCore and flowWorkspace data classes
cytoset_to_list | Methods for conversion between flowCore and flowWorkspace data classes

## -- D --

delete_gs | delete the archive of 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 be different from one another.

## -- E --

estimateLogicle | Compute logicle transformation from the flowData associated with a GatingHierarchy
estimateLogicle-method | Compute logicle transformation from the flowData associated with a GatingHierarchy
estimateLogicle.GatingHierarchy | Compute logicle transformation from the flowData associated with a GatingHierarchy
extract_cluster_pop_name_from_node | Extract the population name from the node path It strips the parent path and cluster method name.

## -- F --

filterObject | convert flowCore filter to a list It convert the flowCore gate to a list whose structure can be understood by underlying c++ data structure.
filterObject-method | convert flowCore filter to a list It convert the flowCore gate to a list whose structure can be understood by underlying c++ data structure.
filter_to_list | convert flowCore filter to a list It convert the flowCore gate to a list whose structure can be understood by underlying c++ data structure.
filter_to_list-method | convert flowCore filter to a list It convert the flowCore gate to a list whose structure can be understood by underlying c++ data structure.
flowData | Fetch or replace the flowData object associated with a GatingSet .
flowData-method | Fetch or replace the flowData object associated with a GatingSet .
flowData<- | Fetch or replace the flowData object associated with a GatingSet .
flowData<--method | Fetch or replace the flowData object associated with a GatingSet .
flowFrame_to_cytoframe | Methods for conversion between flowCore and flowWorkspace data classes
flowJo.fasinh | inverse hyperbolic sine transform function
flowJo.flog | flog transform function
flowJo.fsinh | inverse hyperbolic sine transform function
flowJoTrans | construct the flowJo-type biexponentioal transformation function
flowjo_biexp | construct the flowJo-type biexponentioal transformation function
flowJo_biexp_trans | flowJo biexponential transformation.
flowjo_biexp_trans | flowJo biexponential transformation.
flowjo_fasinh | inverse hyperbolic sine transform function
flowJo_fasinh_trans | flowJo inverse hyperbolic sine transformation.
flowjo_fasinh_trans | flowJo inverse hyperbolic sine transformation.
flowjo_flog | flog transform function
flowjo_fsinh | inverse hyperbolic sine transform function
flowjo_log_trans | flog transform function
flowSet_to_cytoset | Methods for conversion between flowCore and flowWorkspace data classes
flowSet_to_list | Methods for conversion between flowCore and flowWorkspace data classes
flowWorkspace | Import and replicate flowJo workspaces and gating schemes using flowCore.
flowWorkspace-deprecated | Deprecated functions in package 'flowWorkspace'.
flow_breaks | Generate the breaks that makes sense for flow data visualization
flow_trans | helper function to generate a trans objects Used by other specific trans constructor
flush_meta | Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)

## -- G --

GatingHierarchy | Class GatingHierarchy
GatingHierarchy-class | Class GatingHierarchy
GatingSet | Class '"GatingSet"'
GatingSet-class | Class '"GatingSet"'
GatingSet-method | constructors for GatingSet
GatingSet-method | Construct a 'GatingSet' using a template
GatingSet-methods | constructors for GatingSet
GatingSetList | Class '"GatingSetList"'
GatingSetList-class | Class '"GatingSetList"'
getChildren | Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
getChildren-method | Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
getCompensationMatrices | Retrieve the compensation matrices from a 'GatingHierarchy' or 'GatingSet'
getCompensationMatrices-method | Retrieve the compensation matrices from a 'GatingHierarchy' or 'GatingSet'
getData | get gated flow data from a GatingHierarchy/GatingSet/GatingSetList
getData-method | get gated flow data from a GatingHierarchy/GatingSet/GatingSetList
getDescendants | get all the descendant nodes for the given ancester
getDescendants-method | get all the descendant nodes for the given ancester
getGate | Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet.
getGate-method | Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet.
getIndices | Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
getIndices-method | Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
getNodes | Get the names of all nodes from a gating hierarchy.
getNodes-method | Get the names of all nodes from a gating hierarchy.
getParent | Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
getParent-method | Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
getPopStats | Compare the stats(count/freq) between the version parsed from xml and the one recalculated/gated from R
getPopStats-method | Compare the stats(count/freq) between the version parsed from xml and the one recalculated/gated from R
getPopStats-method | Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
getProp | Get count or proportion from populations
getSingleCellExpression | Return the cell events data that express in any of the single populations defined in 'y'
getSingleCellExpressionByGate | Return the cell events data that express in any of the single populations defined in 'y'
getStats | Extract stats from populations(or nodes)
getStats-method | Extract stats from populations(or nodes)
getTotal | Get count or proportion from populations
getTransformations | Return a list of transformations or a transformation in a GatingHierarchy
getTransformations-method | Return a list of transformations or a transformation in a GatingHierarchy
get_cytoframe_from_cs | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
get_default_backend | get/set the default backend format of cytoframe
get_leaf_nodes | get all the leaf nodes
get_log_level | get/set the log level
gh_apply_to_cs | Construct a 'GatingSet' using a template
gh_apply_to_new_fcs | Construct a 'GatingSet' using a template and FCS files
gh_cleanup | Remove on-disk files associatated with flowWorkspace data classes
gh_cleanup_temp | Remove temporary files associatated with flowWorkspace data classes
gh_copy_gate | Copy a node along with all of its descendant nodes to the given ancestor
gh_get_cluster_labels | Retrieve the cluster labels from the cluster nodes
gh_get_compensations | Retrieve the compensation matrices from a 'GatingHierarchy' or 'GatingSet'
gh_get_leaf_nodes | get all the leaf nodes
gh_get_pop_paths | Get the names of all nodes from a gating hierarchy.
gh_get_transformations | Return a list of transformations or a transformation in a GatingHierarchy
gh_keyword_delete | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gh_keyword_insert | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gh_keyword_rename | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gh_keyword_set | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gh_plot_pop_count_cv | Plot the coefficient of variation between xml and openCyto population statistics for each population in a gating hierarchy.
gh_pop_compare_stats | Compare the stats(count/freq) between the version parsed from xml and the one recalculated/gated from R
gh_pop_get_children | Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
gh_pop_get_cluster_name | check if a node is clustering node
gh_pop_get_count | Get count or proportion from populations
gh_pop_get_data | get gated flow data from a GatingHierarchy/GatingSet/GatingSetList
gh_pop_get_descendants | get all the descendant nodes for the given ancester
gh_pop_get_full_path | convert the partial gating path to the full path
gh_pop_get_gate | Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet.
gh_pop_get_indices | Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
gh_pop_get_indices_mat | Return the single-cell matrix of 1/0 dichotomized expression
gh_pop_get_parent | Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
gh_pop_get_proportion | Get count or proportion from populations
gh_pop_get_stats | Extract stats from populations(or nodes)
gh_pop_get_stats_tfilter | Extract stats from populations(or nodes) within a restricted time window
gh_pop_is_bool_gate | The flags of gate nodes
gh_pop_is_gated | The flags of gate nodes
gh_pop_is_hidden | The flags of gate nodes
gh_pop_is_negated | The flags of gate nodes
gh_pop_move | move a node along with all of its descendant nodes to the given ancester
gh_pop_remove | Add populations to a GatingHierarchy
gh_pop_set_gate | update the gate
gh_pop_set_indices | directly update event indices without changing gates
gh_pop_set_name | Update the name of one node in a gating hierarchy/GatingSet.
gh_pop_set_visibility | hide/unhide a node
gh_pop_set_xml_count | save the event counts parsed from xml into c++ tree structure
groupByChannels | split GatingSets into groups based on their flow channels
groupByTree | split GatingSets into groups based on their gating schemes Be careful that the splitted resluts still points to the original data set!!
gslist_to_gs | Merge a GatingSetList into a single GatingSet
gs_check_redundant_nodes | try to determine the redundant terminal(or leaf) nodes that can be removed
gs_cleanup | Remove on-disk files associatated with flowWorkspace data classes
gs_cleanup_temp | Remove temporary files associatated with flowWorkspace data classes
gs_cyto_data | Fetch or replace the flowData object associated with a GatingSet .
gs_cyto_data-method | Fetch or replace the flowData object associated with a GatingSet .
gs_cyto_data<- | Fetch or replace the flowData object associated with a GatingSet .
gs_cyto_data<--method | Fetch or replace the flowData object associated with a GatingSet .
gs_get_compensations | Retrieve the compensation matrices from a 'GatingHierarchy' or 'GatingSet'
gs_get_compensation_internal | extract compensation object from GatingSet
gs_get_cytoframe | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
gs_get_leaf_nodes | get all the leaf nodes
gs_get_pop_paths | Get the names of all nodes from a gating hierarchy.
gs_get_singlecell_expression | Return the cell events data that express in any of the single populations defined in 'y'
gs_get_singlecell_expression_by_gate | Return the cell events data that express in any of the single populations defined in 'y'
gs_get_uri | Return the path of the underlying data files
gs_is_h5 | determine whether the flow data associated with a GatingSet is persistent(on-disk) or in-memory
gs_is_persistent | determine whether the flow data associated with a GatingSet is persistent(on-disk) or in-memory
gs_keyword_delete | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gs_keyword_insert | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gs_keyword_rename | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gs_keyword_set | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects
gs_plot_diff_tree | visualize the tree structure differnece among the GatingSets
gs_plot_pop_count_cv | Plot the coefficient of variation between xml and openCyto population statistics for each population in a gating hierarchy.
gs_pop_add | Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
gs_pop_get_children | Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
gs_pop_get_count_fast | Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
gs_pop_get_count_with_meta | Return a table of population statistics for all populations in a GatingHierarchy/GatingSet or the population proportions or the total number of events of a node (population) in a GatingHierarchy
gs_pop_get_data | get gated flow data from a GatingHierarchy/GatingSet/GatingSetList
gs_pop_get_gate | Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet.
gs_pop_get_gs | subset gs by population node
gs_pop_get_parent | Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy
gs_pop_get_stats | Extract stats from populations(or nodes)
gs_pop_get_stats_tfilter | Extract stats from populations(or nodes) within a restricted time window
gs_pop_remove | Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
gs_pop_set_gate | update the gate
gs_pop_set_name | Update the name of one node in a gating hierarchy/GatingSet.
gs_pop_set_visibility | hide/unhide a node
gs_remove_redundant_channels | Remove the channels from flow data that are not used by gates
gs_remove_redundant_nodes | Remove the terminal leaf nodes that make the gating trees to be different from one another.
gs_split_by_channels | split GatingSets into groups based on their flow channels
gs_split_by_tree | split GatingSets into groups based on their gating schemes Be careful that the splitted resluts still points to the original data set!!
gs_update_channels | Update the channel information of a GatingSet (c++ part)

## -- I --

identifier | Retrieve/replace the GUID of a GatingSet or GatingSetList
identifier-method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
identifier-method | Retrieve/replace the GUID of a GatingSet or GatingSetList
identifier-methods | Retrieve/replace the GUID of a GatingSet or GatingSetList
identifier<--method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
identifier<--method | Retrieve/replace the GUID of a GatingSet or GatingSetList
isGated | The flags of gate nodes
isHidden | The flags of gate nodes
isNcdf | determine whether the flow data associated with a GatingSet is persistent(on-disk) or in-memory
isNegated | The flags of gate nodes
is_tiledb_support | check whether cytolib is build with tiledb support

## -- K --

keyword | Retrieve a specific keyword for a specific sample in a 'GatingHierarchy' or or set of samples in a 'GatingSet' or 'GatingSetList'
keyword-method | 'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
keyword-method | Retrieve a specific keyword for a specific sample in a 'GatingHierarchy' or or set of samples in a 'GatingSet' or 'GatingSetList'
keyword-mutators | Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects

## -- L --

lapply | apply 'FUN' to each sample (i.e. 'GatingHierarchy' or 'cytoframe') in a 'GatingSet' or 'cytoset'
lapply-method | apply 'FUN' to each sample (i.e. 'GatingHierarchy' or 'cytoframe') in a 'GatingSet' or 'cytoset'
lapply-methods | apply 'FUN' to each sample (i.e. 'GatingHierarchy' or 'cytoframe') in a 'GatingSet' or 'cytoset'
length | Methods to get the length of a GatingSet
length-method | Methods to get the length of a GatingSet
load_cytoframe | Load the cytoframe from disk
load_cytoframe_from_fcs | Read a single FCS file in to a cytoframe
load_cytoset | save/load a cytoset to/from disk. load_cytoset() can load a cytoset from either the archive previously saved by save_cytoset() call or from a folder that contains a collection of inidivudal cytoframe files (either in h5 format or tiledb format)
load_cytoset_from_fcs | Read one or several FCS files in to a cytoset
load_gs | save/load a GatingSet/GatingSetList to/from disk.
load_gslist | save/load a GatingSet/GatingSetList to/from disk.
load_meta | Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
lock | Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
logicleGml2_trans | GatingML2 version of logicle transformation.
logicle_trans | logicle transformation.
logtGml2_trans | Gating-ML 2.0 Log transformation.

## -- M --

markernames | Get/set the column(channel) or marker names
markernames-method | 'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
markernames-method | Get/set the column(channel) or marker names
markernames<--method | 'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
markernames<--method | Get/set the column(channel) or marker names
markernmaes<--method | Get/set the column(channel) or marker names
merge-GatingSet | The tools to standardize the tree structures and channel names.
merge_list_to_gs | Merge a list of GatingSets into a single GatingSet
moveNode | move a node along with all of its descendant nodes to the given ancester

## -- N --

ncFlowSet | Fetch the flowData object associated with a GatingSet .
ncFlowSet-method | Fetch the flowData object associated with a GatingSet .
ncFlowSet<- | Fetch the flowData object associated with a GatingSet .
ncFlowSet<--method | Fetch the flowData object associated with a GatingSet .
nodeflags | The flags of gate nodes

## -- O --

openWorkspace | It is now moved along with entire flowJo parser to CytoML package

## -- P --

pData | read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'
pData-method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
pData-method | read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'
pData-methods | read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'
pData<- | read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'
pData<--method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
pData<--method | read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'
phenoData-method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
phenoData<--method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
plot | plot a gating tree
plot-method | plot a gating tree
plot-methods | plot a gating tree
plotGate | Plot gates and associated cell population contained in a 'GatingHierarchy' or 'GatingSet'
plotGate-method | Plot gates and associated cell population contained in a 'GatingHierarchy' or 'GatingSet'
plotGate-methods | Plot gates and associated cell population contained in a 'GatingHierarchy' or 'GatingSet'
plotGate-methods-defunct | Plot gates and associated cell population contained in a 'GatingHierarchy' or 'GatingSet'
pop.MFI | built-in stats functions.
pop_add | Add populations to a GatingHierarchy
pop_add.factor | Add populations to a GatingHierarchy
pop_add.filter | Add populations to a GatingHierarchy
pop_add.filters | Add populations to a GatingHierarchy
pop_add.logical | Add populations to a GatingHierarchy
pop_add.logicalFilterResult | Add populations to a GatingHierarchy
pop_add.multipleFilterResult | Add populations to a GatingHierarchy
pop_add.quadGate | Add populations to a GatingHierarchy
prettyAxis | Determine tick mark locations and labels for a given channel axis

## -- R --

rbind2-method | Merge a GatingSetList into a single GatingSet
realize_view | 'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
realize_view-method | 'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
realize_view-method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
recompute | Compute the cell events by the gates stored within the gating tree.
recompute.GatingSet | Compute the cell events by the gates stored within the gating tree.
recompute.GatingSetList | Compute the cell events by the gates stored within the gating tree.
Rm | Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
rotate_gate | Simplified geometric rotation of gates associated with nodes
rotate_gate-method | Simplified geometric rotation of gates associated with nodes
rotate_gate.GatingHierarchy | Simplified geometric rotation of gates associated with nodes

## -- S --

sampleNames | Get/update sample names in a GatingSet
sampleNames,cytoset, | Get/update sample names in a GatingSet
sampleNames-method | Get/update sample names in a GatingSet
sampleNames-method | save/load a GatingSet/GatingSetList to/from disk.
sampleNames<- | Get/update sample names in a GatingSet
sampleNames<--method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
sampleNames<--method | Get/update sample names in a GatingSet
save_cytoset | save/load a cytoset to/from disk. load_cytoset() can load a cytoset from either the archive previously saved by save_cytoset() call or from a folder that contains a collection of inidivudal cytoframe files (either in h5 format or tiledb format)
save_gs | save/load a GatingSet/GatingSetList to/from disk.
save_gslist | save/load a GatingSet/GatingSetList to/from disk.
scale_gate | Simplified geometric scaling of gates associated with nodes
scale_gate-method | Simplified geometric scaling of gates associated with nodes
scale_gate.GatingHierarchy | Simplified geometric scaling of gates associated with nodes
setGate | update the gate
setGate-method | update the gate
setNode | Update the name of one node in a gating hierarchy/GatingSet.
setNode-method | Update the name of one node in a gating hierarchy/GatingSet.
setNode-method | hide/unhide a node
set_default_backend | get/set the default backend format of cytoframe
set_log_level | get/set the log level
shift_gate | Simplified geometric translation of gates associated with nodes
shift_gate-method | Simplified geometric translation of gates associated with nodes
shift_gate.GatingHierarchy | Simplified geometric translation of gates associated with nodes
show-method | Class GatingHierarchy
show-method | A class describing logical operation (& or |) of the reference populations
show-method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
show-method | Methods to get the length of a GatingSet
standardize-GatingSet | The tools to standardize the tree structures and channel names.
stats.fun | built-in stats functions.
subset | subset the GatingSet/GatingSetList based on 'pData'
subset.GatingSet | subset the GatingSet/GatingSetList based on 'pData'
swap_data_cols | Swap the colnames Perform some validity checks before returning the updated colnames

## -- T --

transform | tranform the flow data asssociated with the GatingSet
transform-method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
transform-method | tranform the flow data asssociated with the GatingSet
transformerList | Constructor for transformerList object
transform_gate | Simplified geometric transformations of gates associated with nodes
transform_gate-method | Simplified geometric transformations of gates associated with nodes
transform_gate.GatingHierarchy | Simplified geometric transformations of gates associated with nodes

## -- U --

updateChannels | Update the channel information of a GatingSet (c++ part)
updateIndices | directly update event indices without changing gates
updateIndices-method | directly update event indices without changing gates

## -- misc --

[ | Bracket operators on 'GatingSet' and 'GatingSetList' objects
[-method | Bracket operators on 'GatingSet' and 'GatingSetList' objects
[-method | 'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame'
[-method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
[[ | Bracket operators on 'GatingSet' and 'GatingSetList' objects
[[-method | Bracket operators on 'GatingSet' and 'GatingSetList' objects
[[-method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'
[[<--method | Bracket operators on 'GatingSet' and 'GatingSetList' objects
[[<--method | 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet'