Package: flowWorkspace 4.17.0
Greg Finak
flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.
This package is designed to facilitate comparison of automated gating methods against manual gating done in flowJo. This package allows you to import basic flowJo workspaces into BioConductor and replicate the gating from flowJo using the flowCore functionality. Gating hierarchies, groups of samples, compensation, and transformation are performed so that the output matches the flowJo analysis.
Authors:
flowWorkspace_4.17.0.tar.gz
flowWorkspace_4.17.0.zip(r-4.5)flowWorkspace_4.17.0.zip(r-4.4)flowWorkspace_4.17.0.zip(r-4.3)
flowWorkspace_4.17.0.tgz(r-4.4-x86_64)flowWorkspace_4.17.0.tgz(r-4.3-x86_64)
flowWorkspace_4.17.0.tar.gz(r-4.5-noble)flowWorkspace_4.17.0.tar.gz(r-4.4-noble)
flowWorkspace.pdf |flowWorkspace.html✨
flowWorkspace/json (API)
NEWS
| # Install 'flowWorkspace' in R: |
| install.packages('flowWorkspace', repos = c('https://bioc.r-universe.dev', 'https://cloud.r-project.org')) |
On BioConductor:flowWorkspace-4.17.0(bioc 3.20)flowWorkspace-4.16.0(bioc 3.19)
This package does not link to any Github/Gitlab/R-forge repository. No issue tracker or development information is available.
Last updated 2 months agofrom:cdae1b1459
Exports:.getNodeIndaddasinh_Gml2asinhtGml2_transbooleanFiltercf_append_colscf_cleanupcf_cleanup_tempcf_flush_metacf_get_h5_file_pathcf_get_uricf_is_subsettedcf_keyword_deletecf_keyword_insertcf_keyword_renamecf_keyword_setcf_load_metacf_lockcf_rename_channelcf_rename_markercf_swap_colnamescf_unlockcf_write_diskcf_write_h5char2booleanFiltercheckRedundantNodescolnamescolnames<-compensateconvert_backendconvert_legacy_gsconvert_legacy_gslistcopyNodecs_add_cytoframecs_cleanup_tempcs_flush_metacs_get_cytoframecs_get_h5_file_pathcs_get_urics_is_subsettedcs_keyword_deletecs_keyword_insertcs_keyword_renamecs_keyword_setcs_load_metacs_lockcs_set_cytoframecs_swap_colnamescs_unlockcytoframe_to_flowFramecytosetcytoset_to_flowSetcytoset_to_listdelete_gsdropRedundantChannelsdropRedundantNodesextract_cluster_pop_name_from_nodefilter_to_listfilterObjectflow_breaksflow_transflowDataflowData<-flowFrame_to_cytoframeflowjo_biexpflowjo_biexp_transflowJo_biexp_transflowjo_fasinhflowjo_fasinh_transflowJo_fasinh_transflowjo_fsinhflowjo_log_transflowJo.fasinhflowJo.flogflowJo.fsinhflowJoTransflowSet_to_cytosetGatingSetGatingSetListget_cytoframe_from_csget_default_backendget_leaf_nodesget_log_levelgetChildrengetCompensationMatricesgetDatagetDescendantsgetGategetIndicesgetNodesgetParentgetPopStatsgetPropgetSingleCellExpressiongetSingleCellExpressionByGategetStatsgetTotalgetTransformationsgh_apply_to_csgh_apply_to_new_fcsgh_cleanup_tempgh_copy_gategh_get_cluster_labelsgh_get_compensationsgh_get_leaf_nodesgh_get_pop_pathsgh_get_transformationsgh_keyword_deletegh_keyword_insertgh_keyword_renamegh_keyword_setgh_plot_pop_count_cvgh_pop_compare_statsgh_pop_get_childrengh_pop_get_cluster_namegh_pop_get_countgh_pop_get_datagh_pop_get_descendantsgh_pop_get_full_pathgh_pop_get_gategh_pop_get_indicesgh_pop_get_indices_matgh_pop_get_parentgh_pop_get_proportiongh_pop_get_statsgh_pop_get_stats_tfiltergh_pop_is_bool_gategh_pop_is_gatedgh_pop_is_hiddengh_pop_is_negatedgh_pop_movegh_pop_removegh_pop_set_gategh_pop_set_indicesgh_pop_set_namegh_pop_set_visibilitygh_pop_set_xml_countgroupByChannelsgroupByTreegs_check_redundant_nodesgs_cleanup_tempgs_clonegs_copy_tree_onlygs_cyto_datags_cyto_data<-gs_get_compensation_internalgs_get_compensationsgs_get_cytoframegs_get_leaf_nodesgs_get_pop_pathsgs_get_singlecell_expressiongs_get_singlecell_expression_by_gategs_get_urigs_is_h5gs_is_persistentgs_keyword_deletegs_keyword_insertgs_keyword_renamegs_keyword_setgs_plot_diff_treegs_plot_pop_count_cvgs_pop_addgs_pop_get_childrengs_pop_get_count_fastgs_pop_get_count_with_metags_pop_get_datags_pop_get_gategs_pop_get_gsgs_pop_get_parentgs_pop_get_statsgs_pop_get_stats_tfiltergs_pop_removegs_pop_set_gategs_pop_set_namegs_pop_set_visibilitygs_remove_redundant_channelsgs_remove_redundant_nodesgs_split_by_channelsgs_split_by_treegs_update_channelsgslist_to_gsidentifieridentifier<-isGatedisHiddenisNcdfisNegatedkeywordlapplyload_cytoframeload_cytoframe_from_fcsload_cytosetload_cytoset_from_fcsload_gsload_gslistlogicle_translogicleGml2_translogtGml2_transmarkernamesmarkernames<-merge_list_to_gsopenWorkspacepDatapData<-phenoDataphenoData<-plotpop_addpop.MFIprettyAxisrbind2realize_viewrecomputeRmrownamesrownames<-sampleNamessampleNames<-save_cytosetsave_gssave_gslistset_default_backendset_log_levelsetGatesetNodeshowswap_data_colstransformtransformerListupdateChannelsupdateIndices
Dependencies:abindBHBiobaseBiocGenericsclicolorspacecpp11crayoncytolibdata.tableDelayedArraydplyrfansifarverflowCoregenericsggplot2gluegraphgtableIRangesisobandlabelinglatticelifecyclemagrittrMASSMatrixMatrixGenericsmatrixStatsmgcvmunsellncdfFlownlmepillarpkgconfigR6RBGLRColorBrewerRcppRgraphvizRhdf5librlangRProtoBufLibS4ArraysS4VectorsscalesSparseArraytibbletidyselectutf8vctrsviridisLitewithrXMLXVectorzlibbioc
flowWorkspace Introduction: A Package to store and maninpulate gated flow data
Rendered fromflowWorkspace-Introduction.Rmdusingknitr::rmarkdownon Jun 12 2024.Last update: 2024-01-17
Started: 2016-02-05
How to merge/standardize GatingSets
Rendered fromHowToMergeGatingSet.Rmdusingknitr::rmarkdownon Jun 12 2024.Last update: 2024-01-17
Started: 2014-09-17
Readme and manuals
Help Manual
| Help page | Topics |
|---|---|
| Import and replicate flowJo workspaces and gating schemes using flowCore. | flowWorkspace-package flowWorkspace |
| Bracket operators on 'GatingSet' and 'GatingSetList' objects | brackets [ [,GatingSet,ANY,ANY,ANY-method [,GatingSet,ANY-method [,GatingSetList,ANY-method [[ [[,GatingSet,character-method [[,GatingSet,logical-method [[,GatingSet,numeric-method [[<-,GatingSet,ANY,ANY,GatingHierarchy-method |
| inverse hyperbolic sine transform function generator (GatingML 2.0 version) | asinh_Gml2 |
| Inverse hyperbolic sine transformation. | asinhtGml2_trans |
| A class describing logical operation (& or |) of the reference populations | booleanFilter booleanFilter-class char2booleanFilter show,booleanFilter-method |
| Append data columns to a flowFrame | cf_append_cols |
| return the cytoframe backend storage format | cf_backend_type |
| Return the file path of the underlying h5 file | cf_get_h5_file_path cf_get_uri |
| check whether a cytoframe/cytoset is a subsetted(by column or by row) view | cf_is_subsetted cs_is_subsetted |
| Save the cytoframe to disk | cf_write_disk |
| Save the cytoframe as h5 format | cf_write_h5 |
| Remove on-disk files associatated with flowWorkspace data classes | cf_cleanup cleanup cs_cleanup gh_cleanup gs_cleanup |
| Remove temporary files associatated with flowWorkspace data classes | cf_cleanup_temp cleanup_temp cs_cleanup_temp gh_cleanup_temp gs_cleanup_temp |
| compensate the flow data asssociated with the GatingSet | compensate compensate,cytoframe,matrix-method compensate,cytoset,ANY-method compensate,cytoset,list-method compensate,cytoset,matrix-method compensate,GatingSet,ANY-method compensate,GatingSetList,ANY-method |
| Methods for conversion between flowCore and flowWorkspace data classes | convert cytoframe_to_flowFrame cytoset_to_flowSet cytoset_to_list flowFrame_to_cytoframe flowSet_to_cytoset flowSet_to_list |
| convert h5 based gs archive to tiledb | convert_backend |
| convert the legacy GatingSet archive (mixed with R and C++ files) to the new format (C++ only) | convert_legacy_gs convert_legacy_gslist |
| Add a cytoframe to a cytoset | cs_add_cytoframe |
| Return the path of the underlying data files | cs_get_h5_file_path cs_get_uri gs_get_uri |
| update a cytoframe in a cytoset | cs_set_cytoframe |
| 'cytoframe': A reference class for efficiently managing the data representation of a 'flowFrame' | cytoframe cytoframe-class keyword,cytoframe,missing-method markernames,cytoframe-method markernames<-,cytoframe-method realize_view realize_view,cytoframe-method [,cytoframe,ANY-method |
| Methods to change channel and marker names for 'cytoframe' and 'cytoset' objects | cf_rename_channel cf_rename_marker cf_swap_colnames cs_swap_colnames cytoframe-labels |
| 'cytoset': a reference class for efficiently managing the data representation of a 'flowSet' | cs_get_cytoframe cytoset cytoset-class get_cytoframe_from_cs gs_get_cytoframe identifier,cytoset-method identifier<-,cytoset,ANY-method pData,cytoset-method pData<-,cytoset,data.frame-method phenoData,cytoset-method phenoData<-,cytoset,ANY-method realize_view,cytoset-method sampleNames<-,cytoset,ANY-method show,cytoset-method transform,cytoset-method [,cytoset,ANY-method [[,cytoset,ANY-method [[<-,cytoset,ANY,ANY,flowFrame-method |
| delete the archive of GatingSet | delete_gs |
| Compute logicle transformation from the flowData associated with a GatingHierarchy | estimateLogicle estimateLogicle,GatingHierarchy-method estimateLogicle,GatingSet-method estimateLogicle.GatingHierarchy |
| Extract the population name from the node path It strips the parent path and cluster method name. | extract_cluster_pop_name_from_node |
| 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 filterObject,default-method filter_to_list filter_to_list,booleanFilter-method filter_to_list,ellipsoidGate-method filter_to_list,logical-method filter_to_list,polygonGate-method filter_to_list,quadGate-method filter_to_list,rectangleGate-method |
| Generate the breaks that makes sense for flow data visualization | flow_breaks |
| helper function to generate a trans objects Used by other specific trans constructor | flow_trans |
| construct the flowJo-type biexponentioal transformation function | flowJoTrans flowjo_biexp |
| flowJo biexponential transformation. | flowJo_biexp_trans flowjo_biexp_trans |
| inverse hyperbolic sine transform function | flowJo.fasinh flowJo.fsinh flowjo_fasinh flowjo_fsinh |
| flowJo inverse hyperbolic sine transformation. | flowJo_fasinh_trans flowjo_fasinh_trans |
| flog transform function | flowJo.flog flowjo_flog flowjo_log_trans |
| Deprecated functions in package 'flowWorkspace'. | flowWorkspace-deprecated |
| Class GatingHierarchy | GatingHierarchy GatingHierarchy-class show,GatingHierarchy-method |
| Class '"GatingSet"' | GatingSet GatingSet-class |
| constructors for GatingSet | GatingSet,cytoset,ANY-method GatingSet,flowSet,ANY-method GatingSet,flowSet-method GatingSet-methods |
| Class '"GatingSetList"' | GatingSetList GatingSetList-class |
| get/set the default backend format of cytoframe | get_default_backend set_default_backend |
| get/set the log level | get_log_level set_log_level |
| Construct a 'GatingSet' using a template | GatingSet,GatingHierarchy,character-method gh_apply_to_cs |
| Construct a 'GatingSet' using a template and FCS files | gh_apply_to_new_fcs |
| Copy a node along with all of its descendant nodes to the given ancestor | copyNode gh_copy_gate |
| Retrieve the cluster labels from the cluster nodes | gh_get_cluster_labels |
| Retrieve the compensation matrices from a 'GatingHierarchy' or 'GatingSet' | getCompensationMatrices getCompensationMatrices,GatingHierachy-method gh_get_compensations gs_get_compensations |
| Return a list of transformations or a transformation in a GatingHierarchy | getTransformations getTransformations,GatingHierarchy-method gh_get_transformations |
| Plot the coefficient of variation between xml and openCyto population statistics for each population in a gating hierarchy. | gh_plot_pop_count_cv gs_plot_pop_count_cv |
| Compare the stats(count/freq) between the version parsed from xml and the one recalculated/gated from R | getPopStats getPopStats,GatingHierarchy-method gh_pop_compare_stats |
| check if a node is clustering node | gh_pop_get_cluster_name |
| get gated flow data from a GatingHierarchy/GatingSet/GatingSetList | getData getData,GatingHierarchy-method getData,GatingSet-method getData,GatingSetList-method gh_pop_get_data gs_pop_get_data |
| get all the descendant nodes for the given ancester | getDescendants getDescendants,GatingHierarchy-method gh_pop_get_descendants |
| convert the partial gating path to the full path | gh_pop_get_full_path |
| Get the membership indices for each event with respect to a particular gate in a GatingHierarchy | getIndices getIndices,GatingHierarchy,character-method gh_pop_get_indices |
| Return the single-cell matrix of 1/0 dichotomized expression | gh_pop_get_indices_mat |
| Get count or proportion from populations | getProp getTotal gh_pop_get_count gh_pop_get_proportion |
| move a node along with all of its descendant nodes to the given ancester | gh_pop_move moveNode |
| directly update event indices without changing gates | gh_pop_set_indices updateIndices updateIndices,GatingHierarchy,character,logical-method |
| save the event counts parsed from xml into c++ tree structure | gh_pop_set_xml_count |
| try to determine the redundant terminal(or leaf) nodes that can be removed | checkRedundantNodes gs_check_redundant_nodes |
| Fetch or replace the flowData object associated with a GatingSet . | flowData flowData,GatingSet-method flowData<- flowData<-,GatingSet-method gs_cyto_data gs_cyto_data,GatingSet-method gs_cyto_data<- gs_cyto_data<-,GatingSet-method |
| extract compensation object from GatingSet | gs_get_compensation_internal |
| get all the leaf nodes | get_leaf_nodes gh_get_leaf_nodes gs_get_leaf_nodes |
| Get the names of all nodes from a gating hierarchy. | getNodes getNodes,GatingSet-method gh_get_pop_paths gs_get_pop_paths |
| Return the cell events data that express in any of the single populations defined in 'y' | getSingleCellExpression getSingleCellExpressionByGate gs_get_singlecell_expression gs_get_singlecell_expression_by_gate |
| determine whether the flow data associated with a GatingSet is persistent(on-disk) or in-memory | gs_is_h5 gs_is_persistent isNcdf |
| visualize the tree structure differnece among the GatingSets | gs_plot_diff_tree |
| Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet. | add add,default-method gs_pop_add gs_pop_remove Rm |
| 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 | getPopStats,GatingSet-method gs_pop_get_count_fast gs_pop_get_count_with_meta |
| Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet. | getGate getGate,GatingHierarchy,character-method getGate,GatingSet,character-method getGate,GatingSetList,character-method gh_pop_get_gate gs_pop_get_gate |
| subset gs by population node | gs_pop_get_gs |
| Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy | getChildren getChildren,GatingSet,character-method getParent getParent,GatingSet,character-method gh_pop_get_children gh_pop_get_parent gs_pop_get_children gs_pop_get_parent |
| Extract stats from populations(or nodes) | getStats getStats,GatingHierarchy-method getStats,GatingSet-method getStats,GatingSetList-method gh_pop_get_stats gs_pop_get_stats |
| Extract stats from populations(or nodes) within a restricted time window | gh_pop_get_stats_tfilter gs_pop_get_stats_tfilter |
| update the gate | gh_pop_set_gate gs_pop_set_gate setGate setGate,GatingHierarchy,character,filter-method setGate,GatingSet,character,ANY-method |
| Update the name of one node in a gating hierarchy/GatingSet. | gh_pop_set_name gs_pop_set_name setNode setNode,GatingHierarchy,character,ANY-method setNode,GatingHierarchy,character,character-method setNode,GatingSet,character,ANY-method |
| hide/unhide a node | gh_pop_set_visibility gs_pop_set_visibility setNode,GatingHierarchy,character,logical-method |
| Remove the channels from flow data that are not used by gates | dropRedundantChannels gs_remove_redundant_channels |
| Remove the terminal leaf nodes that make the gating trees to be different from one another. | dropRedundantNodes gs_remove_redundant_nodes |
| split GatingSets into groups based on their flow channels | groupByChannels gs_split_by_channels |
| split GatingSets into groups based on their gating schemes Be careful that the splitted resluts still points to the original data set!! | groupByTree gs_split_by_tree |
| Update the channel information of a GatingSet (c++ part) | gs_update_channels updateChannels |
| Merge a GatingSetList into a single GatingSet | gslist_to_gs rbind2,GatingSetList,missing-method |
| Retrieve/replace the GUID of a GatingSet or GatingSetList | identifier identifier,GatingSet-method identifier,GatingSetList-method identifier-methods identifier<-,GatingSet,ANY-method identifier<-,GatingSet,character-method identifier<-,GatingSet-method identifier<-,GatingSetList,ANY-method identifier<-,GatingSetList,character-method |
| Retrieve a specific keyword for a specific sample in a 'GatingHierarchy' or or set of samples in a 'GatingSet' or 'GatingSetList' | keyword keyword,GatingHierarchy,character-method keyword,GatingHierarchy,missing-method keyword,GatingSet,character-method keyword,GatingSet,missing-method keyword,GatingSetList,character-method keyword,GatingSetList,missing-method |
| Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects | cf_keyword_delete cf_keyword_insert cf_keyword_rename cf_keyword_set cs_keyword_delete cs_keyword_insert cs_keyword_rename cs_keyword_set gh_keyword_delete gh_keyword_insert gh_keyword_rename gh_keyword_set gs_keyword_delete gs_keyword_insert gs_keyword_rename gs_keyword_set keyword-mutators |
| apply 'FUN' to each sample (i.e. 'GatingHierarchy' or 'cytoframe') in a 'GatingSet' or 'cytoset' | lapply lapply,cytoset-method lapply,GatingSet-method lapply-methods |
| Methods to get the length of a GatingSet | length length,GatingSet-method show,GatingSet-method |
| Load the cytoframe from disk | load_cytoframe |
| Read a single FCS file in to a cytoframe | load_cytoframe_from_fcs |
| Read one or several FCS files in to a cytoset | load_cytoset_from_fcs |
| Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe) | cf_flush_meta cf_load_meta cs_flush_meta cs_load_meta flush_meta load_meta |
| Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag | cf_lock cf_unlock cs_lock cs_unlock lock |
| logicle transformation. | logicle_trans |
| GatingML2 version of logicle transformation. | logicleGml2_trans |
| Gating-ML 2.0 Log transformation. | logtGml2_trans |
| Get/set the column(channel) or marker names | colnames,cytoframe-method colnames,cytoset-method colnames,GatingHierarchy-method colnames,GatingSet-method colnames<-,cytoframe-method colnames<-,cytoset-method colnames<-,GatingHierarchy-method colnames<-,GatingSet,ANY-method colnames<-,GatingSet-method markernames markernames,cytoset-method markernames,GatingHierarchy-method markernames,GatingSet-method markernames<-,cytoset-method markernames<-,GatingHierarchy-method markernames<-,GatingSet,ANY-method markernames<-,GatingSet-method markernmaes<-,cytoframe-method |
| Merge a list of GatingSets into a single GatingSet | merge_list_to_gs |
| Fetch the flowData object associated with a GatingSet . | ncFlowSet ncFlowSet,GatingSet-method ncFlowSet<- ncFlowSet<-,GatingSet-method |
| The flags of gate nodes | gh_pop_is_bool_gate gh_pop_is_gated gh_pop_is_hidden gh_pop_is_negated isGated isHidden isNegated nodeflags |
| It is now moved along with entire flowJo parser to CytoML package | openWorkspace |
| read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList' | pData pData,GatingHierarchy-method pData,GatingSet-method pData-methods pData<- pData<-,GatingSet,data.frame-method pData<-,GatingSetList,data.frame-method |
| plot a gating tree | plot plot,GatingSet,character-method plot,GatingSet,missing-method plot-methods |
| Add populations to a GatingHierarchy | gh_pop_remove pop_add pop_add.factor pop_add.filter pop_add.filters pop_add.logical pop_add.logicalFilterResult pop_add.multipleFilterResult pop_add.quadGate |
| Determine tick mark locations and labels for a given channel axis | prettyAxis |
| Compute the cell events by the gates stored within the gating tree. | recompute recompute.GatingSet recompute.GatingSetList |
| Simplified geometric rotation of gates associated with nodes | rotate_gate rotate_gate,GatingHierarchy-method rotate_gate,GatingSet-method rotate_gate.GatingHierarchy |
| Get/update sample names in a GatingSet | sampleNames sampleNames,cytoset, sampleNames,cytoset-method sampleNames,GatingSet-method sampleNames<- sampleNames<-,GatingSet,ANY-method sampleNames<-,GatingSet-method |
| save/load a cytoset to/from disk. | load_cytoset save_cytoset |
| save/load a GatingSet/GatingSetList to/from disk. | load_gs load_gslist sampleNames,character-method save_gs save_gslist |
| Simplified geometric scaling of gates associated with nodes | scale_gate scale_gate,GatingHierarchy-method scale_gate,GatingSet-method scale_gate.GatingHierarchy |
| Simplified geometric translation of gates associated with nodes | shift_gate shift_gate,GatingHierarchy-method shift_gate,GatingSet-method shift_gate.GatingHierarchy |
| The tools to standardize the tree structures and channel names. | merge-GatingSet standardize-GatingSet |
| built-in stats functions. | pop.MFI stats.fun |
| subset the GatingSet/GatingSetList based on 'pData' | subset subset.GatingSet |
| Swap the colnames Perform some validity checks before returning the updated colnames | swap_data_cols |
| tranform the flow data asssociated with the GatingSet | transform transform,GatingSet-method transform,GatingSetList-method |
| Simplified geometric transformations of gates associated with nodes | transform_gate transform_gate,GatingHierarchy-method transform_gate,GatingSet-method transform_gate.GatingHierarchy |
| Constructor for transformerList object | transformerList |
