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


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Documentation for package ‘flowWorkspace’ version 4.12.0

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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
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

-- 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
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'