Man pages for flowWorkspace
Infrastructure for representing and interacting with gated and ungated cytometry data sets.
| asinh_Gml2 | inverse hyperbolic sine transform function generator... |
| asinhtGml2_trans | Inverse hyperbolic sine transformation. |
| booleanFilter-class | A class describing logical operation (& or |) of the... |
| brackets | Bracket operators on 'GatingSet' and 'GatingSetList' objects |
| cf_append_cols | Append data columns to a flowFrame |
| cf_backend_type | return the cytoframe backend storage format |
| cf_get_uri | Return the file path of the underlying h5 file |
| 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 |
| cleanup | Remove on-disk files associatated with flowWorkspace data... |
| cleanup_temp | Remove temporary files associatated with flowWorkspace data... |
| compensate | compensate the flow data asssociated with the GatingSet |
| convert | Methods for conversion between flowCore and flowWorkspace... |
| convert_backend | convert h5 based gs archive to tiledb |
| convert_legacy | convert the legacy GatingSet archive (mixed with R and C++... |
| cs_add_cytoframe | Add a cytoframe to a cytoset |
| cs_get_uri | Return the path of the underlying data files |
| cs_set_cytoframe | update a cytoframe in a cytoset |
| cytoframe | 'cytoframe': A reference class for efficiently managing the... |
| cytoframe-labels | Methods to change channel and marker names for 'cytoframe'... |
| cytoset | 'cytoset': a reference class for efficiently managing the... |
| default_backend | get/set the default backend format of cytoframe |
| delete_gs | delete the archive of GatingSet |
| estimateLogicle | Compute logicle transformation from the flowData associated... |
| extract_cluster_pop_name_from_node | Extract the population name from the node path It strips the... |
| filter_to_list | convert flowCore filter to a list It convert the flowCore... |
| flow_breaks | Generate the breaks that makes sense for flow data... |
| flowjo_biexp | construct the flowJo-type biexponentioal transformation... |
| flowjo_biexp_trans | flowJo biexponential transformation. |
| flowjo_fasinh | inverse hyperbolic sine transform function |
| flowjo_fasinh_trans | flowJo inverse hyperbolic sine transformation. |
| flowjo_log_trans | flog transform function |
| flow_trans | helper function to generate a trans objects Used by other... |
| flowWorkspace-deprecated | Deprecated functions in package 'flowWorkspace'. |
| flowWorkspace-package | Import and replicate flowJo workspaces and gating schemes... |
| GatingHierarchy-class | Class GatingHierarchy |
| GatingSet-class | Class '"GatingSet"' |
| GatingSetList-class | Class '"GatingSetList"' |
| GatingSet-methods | constructors for GatingSet |
| 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_copy_gate | Copy a node along with all of its descendant nodes to the... |
| gh_get_cluster_labels | Retrieve the cluster labels from the cluster nodes |
| gh_get_compensations | Retrieve the compensation matrices from a 'GatingHierarchy'... |
| gh_get_transformations | Return a list of transformations or a transformation in a... |
| gh_pop_compare_stats | Compare the stats(count/freq) between the version parsed from... |
| gh_pop_get_cluster_name | check if a node is clustering node |
| gh_pop_get_data | get gated flow data from a... |
| 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_indices | Get the membership indices for each event with respect to a... |
| gh_pop_get_indices_mat | Return the single-cell matrix of 1/0 dichotomized expression |
| gh_pop_get_proportion | Get count or proportion from populations |
| gh_pop_move | move a node along with all of its descendant nodes to the... |
| gh_pop_set_indices | directly update event indices without changing gates |
| gh_pop_set_xml_count | save the event counts parsed from xml into c++ tree structure |
| gs_check_redundant_nodes | try to determine the redundant terminal(or leaf) nodes that... |
| gs_cyto_data | Fetch or replace the flowData object associated with a... |
| gs_get_compensation_internal | extract compensation object from GatingSet |
| 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... |
| gs_is_persistent | determine whether the flow data associated with a GatingSet... |
| gslist_to_gs | Merge a GatingSetList into a single GatingSet |
| 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... |
| gs_pop_add | Create a GatingSet and add/remove the flowCore gate(or... |
| gs_pop_get_children | Return the name of the parent population or a list of child... |
| gs_pop_get_count_fast | Return a table of population statistics for all populations... |
| gs_pop_get_gate | Return the flowCore gate definition associated with a node in... |
| gs_pop_get_gs | subset gs by population node |
| gs_pop_get_stats | Extract stats from populations(or nodes) |
| gs_pop_get_stats_tfilter | Extract stats from populations(or nodes) within a restricted... |
| 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... |
| 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... |
| gs_update_channels | Update the channel information of a GatingSet (c++ part) |
| identifier-methods | Retrieve/replace the GUID of a GatingSet or GatingSetList |
| is_subsetted | check whether a cytoframe/cytoset is a subsetted(by column or... |
| is_tiledb_support | check whether cytolib is build with tiledb support |
| keyword | Retrieve a specific keyword for a specific sample in a... |
| keyword-mutators | Methods to alter keywords in 'cytoframe', 'cytoset',... |
| lapply-methods | apply 'FUN' to each sample (i.e. 'GatingHierarchy' or... |
| length | 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_from_fcs | Read one or several FCS files in to a cytoset |
| load_meta | Flush/load meta data (keywords, pData, channels/markers)... |
| lock | Lock/Unlock the cytoset/cytoframe by turning on/off its... |
| logicleGml2_trans | GatingML2 version of logicle transformation. |
| logicle_trans | logicle transformation. |
| loglevel | get/set the log level |
| logtGml2_trans | Gating-ML 2.0 Log transformation. |
| markernames | Get/set the column(channel) or marker names |
| merge_list_to_gs | Merge a list of GatingSets into a single GatingSet |
| ncFlowSet-methods | Fetch the flowData object associated with a GatingSet . |
| nodeflags | The flags of gate nodes |
| openWorkspace | It is now moved along with entire flowJo parser to CytoML... |
| pData-methods | read/set pData of flow data associated with... |
| plotGate-methods-defunct | Plot gates and associated cell population contained in a... |
| plot-methods | plot a gating tree |
| pop_add | Add populations to a GatingHierarchy |
| prettyAxis | Determine tick mark locations and labels for a given channel... |
| recompute | Compute the cell events by the gates stored within the gating... |
| rotate_gate | Simplified geometric rotation of gates associated with nodes |
| sampleNames | Get/update sample names in a GatingSet |
| save_cytoset | save/load a cytoset to/from disk. load_cytoset() can load a... |
| save_gs | save/load a GatingSet/GatingSetList to/from disk. |
| scale_gate | Simplified geometric scaling of gates associated with nodes |
| shift_gate | Simplified geometric translation of gates associated with... |
| standardize-GatingSet | The tools to standardize the tree structures and channel... |
| stats.fun | built-in stats functions. |
| subset | subset the GatingSet/GatingSetList based on 'pData' |
| swap_data_cols | Swap the colnames Perform some validity checks before... |
| transform | tranform the flow data asssociated with the GatingSet |
| transformerList | Constructor for transformerList object |
| transform_gate | Simplified geometric transformations of gates associated with... |
