| 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 |
| 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) |
| 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) |
| 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 |
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