Function reference • flowWorkspace

GatingHierarchy and GatingSet classes Classes for managing compensation, transformation, and gating of cytometry data (FCS files) and methods for creating them
`GatingHierarchy-class`	Class GatingHierarchy
`GatingSet-class`	Class `"GatingSet"`
`GatingSet(<cytoset>,<ANY>)`	constructors for GatingSet
`GatingSetList()`	Class `"GatingSetList"`
`[`(<GatingSet>,<ANY>,<ANY>,<ANY>) `[[`(<GatingSet>,<numeric>)	Bracket operators on `GatingSet` and `GatingSetList` objects
`identifier()` `identifier<-`(<GatingSet>,<ANY>) `identifier<-`(<GatingSetList>,<character>)	Retrieve/replace the GUID of a GatingSet or GatingSetList
`convert_legacy_gs()` `convert_legacy_gslist()`	convert the legacy GatingSet archive (mixed with R and C++ files) to the new format (C++ only)
cytoframe and cytoset classes Reference classes for efficiently managing the representation of data from FCS files (analagous to flowFrame and flowSet classes from the flowCore package)
`cytoframe`	`cytoframe`: A reference class for efficiently managing the data representation of a `flowFrame`
`cytoset`	`cytoset`: a reference class for efficiently managing the data representation of a `flowSet`
`cytoframe_to_flowFrame()` `flowFrame_to_cytoframe()` `cytoset_to_flowSet()` `flowSet_to_cytoset()` `cytoset_to_list()`	Methods for conversion between flowCore and flowWorkspace data classes
`load_cytoframe_from_fcs()`	Read a single FCS file in to a cytoframe
`cf_get_uri()` `cf_get_h5_file_path()`	Return the file path of the underlying h5 file
`cf_write_h5()`	Save the cytoframe as h5 format
`load_cytoset_from_fcs()`	Read one or several FCS files in to a cytoset
`save_cytoset()` `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)
`cs_add_cytoframe()`	Add a cytoframe to a cytoset
`cs_set_cytoframe()`	update a cytoframe in a cytoset
`cs_get_uri()` `cs_get_h5_file_path()` `gs_get_uri()`	Return the path of the underlying data files
`cf_flush_meta()` `cf_load_meta()` `cs_flush_meta()` `cs_load_meta()`	Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)
`cf_lock()` `cf_unlock()` `cs_lock()` `cs_unlock()`	Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag
`cf_append_cols()`	Append data columns to a flowFrame
`cf_swap_colnames()` `cf_rename_channel()` `cf_rename_marker()` `cs_swap_colnames()`	Methods to change channel and marker names for `cytoframe` and `cytoset` objects
`cf_keyword_insert()` `cf_keyword_delete()` `cf_keyword_rename()` `cf_keyword_set()` `cs_keyword_insert()` `cs_keyword_delete()` `cs_keyword_rename()` `cs_keyword_set()` `gh_keyword_insert()` `gh_keyword_delete()` `gh_keyword_rename()` `gh_keyword_set()` `gs_keyword_insert()` `gs_keyword_delete()` `gs_keyword_rename()` `gs_keyword_set()`	Methods to alter keywords in `cytoframe`, `cytoset`, `GatingHierarchy`, or `GatingSet` objects
Examining the hierarchical gating tree Functions for examining the subpopulations resulting from applying gates to the data
`plot()`	plot a gating tree
`gs_plot_diff_tree()`	visualize the tree structure differnece among the GatingSets
`gs_get_pop_paths()` `gh_get_pop_paths()`	Get the names of all nodes from a gating hierarchy.
`gs_get_leaf_nodes()` `gh_get_leaf_nodes()`	get all the leaf nodes
`gs_check_redundant_nodes()`	try to determine the redundant terminal(or leaf) nodes that can be removed
`gs_remove_redundant_nodes()`	Remove the terminal leaf nodes that make the gating trees to be different from one another.
`gh_get_cluster_labels()`	Retrieve the cluster labels from the cluster nodes
`gh_pop_get_cluster_name()`	check if a node is clustering node
`extract_cluster_pop_name_from_node()`	Extract the population name from the node path It strips the parent path and cluster method name.
`gh_pop_get_full_path()`	convert the partial gating path to the full path
`gs_pop_get_parent()` `gh_pop_get_parent()` `gs_pop_get_children()` `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_descendants()`	get all the descendant nodes for the given ancester
`gs_pop_get_stats()` `gh_pop_get_stats()`	Extract stats from populations(or nodes)
`gs_pop_get_stats_tfilter()` `gh_pop_get_stats_tfilter()`	Extract stats from populations(or nodes) within a restricted time window
`gh_pop_compare_stats()`	Compare the stats(count/freq) between the version parsed from xml and the one recalculated/gated from R
`gh_plot_pop_count_cv()` `gs_plot_pop_count_cv()`	Plot the coefficient of variation between xml and openCyto population statistics for each population in a gating hierarchy.
`gh_pop_get_proportion()` `gh_pop_get_count()`	Get count or proportion from populations
`gs_pop_get_count_fast()` `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
Accessing underyling data Functions for accessing or altering the flowFrame or flowSet objects underlying the gating analysis. These can also be useful in preparing GatingSet objects for merging.
`gs_is_persistent()` `gs_is_h5()` `isNcdf()`	determine whether the flow data associated with a GatingSet is persistent(on-disk) or in-memory
`gs_cyto_data()` `gs_cyto_data<-`()	Fetch or replace the flowData object associated with a GatingSet .
`gh_pop_get_data()`	get gated flow data from a GatingHierarchy/GatingSet/GatingSetList
`gh_get_compensations()` `gs_get_compensations()`	Retrieve the compensation matrices from a `GatingHierarchy` or `GatingSet`
`gs_get_compensation_internal()`	extract compensation object from GatingSet
`gh_get_transformations()`	Return a list of transformations or a transformation in a GatingHierarchy
`compensate(<GatingSet>,<ANY>)`	compensate the flow data asssociated with the GatingSet
`transform(<GatingSet>)`	tranform the flow data asssociated with the GatingSet
`length(<GatingSet>)` `show(<GatingSet>)`	Methods to get the length of a GatingSet
`sampleNames()` `sampleNames<-`()	Get/update sample names in a GatingSet
`markernames(<GatingHierarchy>)` `markernames<-`(<GatingHierarchy>) `colnames(<GatingHierarchy>)` `colnames<-`(<GatingHierarchy>)	Get/set the column(channel) or marker names
`pData()` `pData<-`()	read/set pData of flow data associated with `GatingHierarchy`, `GatingSet`, or `GatingSetList`
`keyword(<GatingHierarchy>,<character>)` `keyword(<GatingHierarchy>,<missing>)`	Retrieve a specific keyword for a specific sample in a `GatingHierarchy` or or set of samples in a `GatingSet` or `GatingSetList`
Perform gating analysis Functions for accessing, altering, adding, and removing gate definitions and their resulting subpopulations. These can also be useful in preparing GatingSet objects for merging.
`gh_pop_is_gated()` `gh_pop_is_negated()` `gh_pop_is_hidden()` `gh_pop_is_bool_gate()`	The flags of gate nodes
`gh_pop_set_visibility()` `gs_pop_set_visibility()`	hide/unhide a node
`gh_pop_set_xml_count()`	save the event counts parsed from xml into c++ tree structure
`gh_pop_get_gate()` `gs_pop_get_gate()`	Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet.
`gh_pop_set_gate()` `gs_pop_set_gate()`	update the gate
`recompute()`	Compute the cell events by the gates stored within the gating tree.
`gh_pop_set_name()` `gs_pop_set_name()`	Update the name of one node in a gating hierarchy/GatingSet.
`transform_gate(<GatingHierarchy>)`	Simplified geometric transformations of gates associated with nodes
`rotate_gate(<GatingHierarchy>)`	Simplified geometric rotation of gates associated with nodes
`scale_gate(<GatingHierarchy>)`	Simplified geometric scaling of gates associated with nodes
`shift_gate(<GatingHierarchy>)`	Simplified geometric translation of gates associated with nodes
`subset(<GatingSet>)`	subset the GatingSet/GatingSetList based on 'pData'
`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_set_indices()`	directly update event indices without changing gates
`gs_get_singlecell_expression()` `gs_get_singlecell_expression_by_gate()`	Return the cell events data that express in any of the single populations defined in `y`
`pop.MFI()`	built-in stats functions.
`pop_add()` `gh_pop_remove()`	Add populations to a GatingHierarchy
`gs_pop_add()` `gs_pop_remove()`	Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
`gh_pop_move()`	move a node along with all of its descendant nodes to the given ancester
`gh_copy_gate()`	Copy a node along with all of its descendant nodes to the given ancestor
`gh_apply_to_new_fcs()`	Construct a `GatingSet` using a template and FCS files
`standardize-GatingSet`	The tools to standardize the tree structures and channel names.
`gs_update_channels()`	Update the channel information of a GatingSet (c++ part)
`gs_remove_redundant_channels()`	Remove the channels from flow data that are not used by gates
`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!!
`merge_list_to_gs()`	Merge a list of GatingSets into a single GatingSet
`lapply()`	apply `FUN` to each sample (i.e. `GatingHierarchy` or `cytoframe`) in a `GatingSet` or `cytoset`
`gslist_to_gs()`	Merge a GatingSetList into a single GatingSet
Helpers to generate transformations and filters Functions for quickly constructing transformations or filters or converting them to a form that can be applied to data in a GatingHierachy or GatingSet
`flow_trans()`	helper function to generate a trans objects Used by other specific trans constructor
`transformerList()`	Constructor for transformerList object
`estimateLogicle(<GatingHierarchy>)`	Compute logicle transformation from the flowData associated with a GatingHierarchy
`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.
`asinh_Gml2()`	inverse hyperbolic sine transform function generator (GatingML 2.0 version)
`asinhtGml2_trans()`	Inverse hyperbolic sine transformation.
`logicle_trans()`	logicle transformation.
`logicleGml2_trans()`	GatingML2 version of logicle transformation.
`logtGml2_trans()`	Gating-ML 2.0 Log transformation.
`flowjo_fasinh()` `flowjo_fsinh()`	inverse hyperbolic sine transform function
`flowjo_fasinh_trans()` `flowJo_fasinh_trans()`	flowJo inverse hyperbolic sine transformation.
`flowjo_log_trans()`	flog transform function
`flowjo_biexp()`	construct the flowJo-type biexponentioal transformation function
`flowjo_biexp_trans()` `flowJo_biexp_trans()`	flowJo biexponential transformation.
`booleanFilter()` `char2booleanFilter()`	A class describing logical operation (& or \|) of the reference populations
Read/write GatingSet objects Functions to read save GatingSet objects to disk or read them in to an R session
`save_gs()` `load_gs()` `sampleNames(<character>)` `save_gslist()` `load_gslist()`	save/load a GatingSet/GatingSetList to/from disk.
Plotting functions Methods for plotting the hierarchical gating tree and gates. More dedicated plotting methods for GatingSet and GatingHierarchy objects are provided by the ggcyto package,
`plot()`	plot a gating tree
`plotGate()`	Plot gates and associated cell population contained in a `GatingHierarchy` or `GatingSet`
`prettyAxis()`	Determine tick mark locations and labels for a given channel axis
Miscellaneous helper functions Functions whose role does not easily fit in to one of the above categories
`get_log_level()` `set_log_level()`	get/set the log level
`flow_breaks()`	Generate the breaks that makes sense for flow data visualization
`swap_data_cols()`	Swap the colnames Perform some validity checks before returning the updated colnames
`cf_cleanup_temp()` `cs_cleanup_temp()` `gh_cleanup_temp()` `gs_cleanup_temp()`	Remove temporary files associatated with flowWorkspace data classes

Reference

GatingHierarchy and GatingSet classes

cytoframe and cytoset classes

Examining the hierarchical gating tree

Accessing underyling data

Perform gating analysis

Helpers to generate transformations and filters

Read/write GatingSet objects

Plotting functions

Miscellaneous helper functions