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Gating hierarchies, groups of samples,\ncompensation, and transformation are performed so that the\noutput matches the flowJo analysis.", "License": "AGPL-3.0-only", "License_restricts_use": "no", "LazyLoad": "yes", "Collate": "'cytoframe.R' 'cytoset.R' 'AllClasses.R' 'getStats.R'\n'GatingHierarchy_Methods.R' 'GatingSet_Methods.R'\n'GatingSetList_Methods.R' 'GatingSet_factors.R'\n'filterObject_Methods.R' 'add_Methods.R' 'copyNode.R' 'cpp11.R'\n'cytoset_factors.R' 'deprecated.R' 'flow_trans.R'\n'getDescendants.R' 'getSingleCellExpression.R' 'identifier.R'\n'load_fcs.R' 'load_gs.R' 'merge_GatingSet.R' 'merge_gslist.R'\n'moveNode.R' 'parse_transformer.R' 'setGate_Methods.R'\n'updateIndices.R' 'utils.R' 'zzz.R'", "VignetteBuilder": "knitr", "biocViews": "ImmunoOncology, FlowCytometry, DataImport, Preprocessing,\nDataRepresentation", "SystemRequirements": "GNU make, C++17", "Encoding": "UTF-8", "RoxygenNote": "7.3.3", "Config/pak/sysreqs": "make libxml2-dev libssl-dev zlib1g-dev", 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"extract_cluster_pop_name_from_node" ] }, { "page": "filter_to_list", "title": "convert flowCore filter to a list It convert the flowCore gate to a list whose structure can be understood by underlying c++ data structure.", "topics": [ "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" ] }, { "page": "flow_breaks", "title": "Generate the breaks that makes sense for flow data visualization", "topics": [ "flow_breaks" ] }, { "page": "flow_trans", "title": "helper function to generate a trans objects Used by other specific trans constructor", "topics": [ "flow_trans" ] }, { "page": "flowjo_biexp", "title": "construct the flowJo-type biexponentioal transformation function", "topics": [ "flowJoTrans", "flowjo_biexp" ] }, { "page": "flowjo_biexp_trans", "title": 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"title": "constructors for GatingSet", "topics": [ "GatingSet,cytoset,ANY-method", "GatingSet,flowSet,ANY-method", "GatingSet,flowSet-method", "GatingSet-methods" ] }, { "page": "GatingSetList-class", "title": "Class '\"GatingSetList\"'", "topics": [ "GatingSetList", "GatingSetList-class" ] }, { "page": "default_backend", "title": "get/set the default backend format of cytoframe", "topics": [ "get_default_backend", "set_default_backend" ] }, { "page": "loglevel", "title": "get/set the log level", "topics": [ "get_log_level", "set_log_level" ] }, { "page": "gh_apply_to_cs", "title": "Construct a 'GatingSet' using a template", "topics": [ "GatingSet,GatingHierarchy,character-method", "gh_apply_to_cs" ] }, { "page": "gh_apply_to_new_fcs", "title": "Construct a 'GatingSet' using a template and FCS files", "topics": [ "gh_apply_to_new_fcs" ] }, { "page": "gh_copy_gate", "title": "Copy a node along with all of its descendant nodes to the given ancestor", "topics": [ "copyNode", "gh_copy_gate" ] }, { "page": "gh_get_cluster_labels", "title": "Retrieve the cluster labels from the cluster nodes", "topics": [ "gh_get_cluster_labels" ] }, { "page": "gh_get_compensations", "title": "Retrieve the compensation matrices from a 'GatingHierarchy' or 'GatingSet'", "topics": [ "getCompensationMatrices", "getCompensationMatrices,GatingHierachy-method", "gh_get_compensations", "gs_get_compensations" ] }, { "page": "gh_get_transformations", "title": "Return a list of transformations or a transformation in a GatingHierarchy", "topics": [ "getTransformations", "getTransformations,GatingHierarchy-method", "gh_get_transformations" ] }, { "page": "gs_plot_pop_count_cv", "title": "Plot the coefficient of variation between xml and openCyto population statistics for each population in a gating hierarchy.", "topics": [ "gh_plot_pop_count_cv", "gs_plot_pop_count_cv" ] }, { "page": "gh_pop_compare_stats", "title": "Compare the stats(count/freq) between the version parsed from xml and the one recalculated/gated from R", "topics": [ "getPopStats", "getPopStats,GatingHierarchy-method", "gh_pop_compare_stats" ] }, { "page": "gh_pop_get_cluster_name", "title": "check if a node is clustering node", "topics": [ "gh_pop_get_cluster_name" ] }, { "page": "gh_pop_get_data", "title": "get gated flow data from a GatingHierarchy/GatingSet/GatingSetList", "topics": [ "getData", "getData,GatingHierarchy-method", "getData,GatingSet-method", "getData,GatingSetList-method", "gh_pop_get_data", "gs_pop_get_data" ] }, { "page": "gh_pop_get_descendants", "title": "get all the descendant nodes for the given ancester", "topics": [ "getDescendants", "getDescendants,GatingHierarchy-method", "gh_pop_get_descendants" ] }, { "page": "gh_pop_get_full_path", "title": "convert the partial gating path to the full path", "topics": [ "gh_pop_get_full_path" ] }, { "page": "gh_pop_get_indices", "title": "Get the membership indices for each event with respect to a particular gate in a GatingHierarchy", "topics": [ "getIndices", "getIndices,GatingHierarchy,character-method", "gh_pop_get_indices" ] }, { "page": "gh_pop_get_indices_mat", "title": "Return the single-cell matrix of 1/0 dichotomized expression", "topics": [ "gh_pop_get_indices_mat" ] }, { "page": "gh_pop_get_proportion", "title": "Get count or proportion from populations", "topics": [ "getProp", "getTotal", "gh_pop_get_count", "gh_pop_get_proportion" ] }, { "page": "gh_pop_move", "title": "move a node along with all of its descendant nodes to the given ancester", "topics": [ "gh_pop_move", "moveNode" ] }, { "page": "gh_pop_set_indices", "title": "directly update event indices without changing gates", "topics": [ "gh_pop_set_indices", "updateIndices", "updateIndices,GatingHierarchy,character,logical-method" ] }, { "page": "gh_pop_set_xml_count", "title": "save the event counts parsed from xml into c++ tree structure", "topics": [ "gh_pop_set_xml_count" ] }, { "page": "gs_check_redundant_nodes", "title": "try to determine the redundant terminal(or leaf) nodes that can be removed", "topics": [ "checkRedundantNodes", "gs_check_redundant_nodes" ] }, { "page": "gs_cyto_data", "title": "Fetch or replace the flowData object associated with a GatingSet .", "topics": [ "flowData", "flowData,GatingSet-method", "flowData<-", "flowData<-,GatingSet-method", "gs_cyto_data", "gs_cyto_data,GatingSet-method", "gs_cyto_data<-", "gs_cyto_data<-,GatingSet-method" ] }, { "page": "gs_get_compensation_internal", "title": "extract compensation object from GatingSet", "topics": [ "gs_get_compensation_internal" ] }, { "page": "gs_get_leaf_nodes", "title": "get all the leaf nodes", "topics": [ "get_leaf_nodes", "gh_get_leaf_nodes", "gs_get_leaf_nodes" ] }, { "page": "gs_get_pop_paths", "title": "Get the names of all nodes from a gating hierarchy.", "topics": [ "getNodes", "getNodes,GatingSet-method", "gh_get_pop_paths", "gs_get_pop_paths" ] }, { "page": "gs_get_singlecell_expression", "title": "Return the cell events data that express in any of the single populations defined in 'y'", "topics": [ "getSingleCellExpression", "getSingleCellExpressionByGate", "gs_get_singlecell_expression", "gs_get_singlecell_expression_by_gate" ] }, { "page": "gs_is_persistent", "title": "determine whether the flow data associated with a GatingSet is persistent(on-disk) or in-memory", "topics": [ "gs_is_h5", "gs_is_persistent", "isNcdf" ] }, { "page": "gs_plot_diff_tree", "title": "visualize the tree structure differnece among the GatingSets", "topics": [ "gs_plot_diff_tree" ] }, { "page": "gs_pop_add", "title": "Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.", "topics": [ "add", "add,default-method", "gs_pop_add", "gs_pop_remove", "Rm" ] }, { "page": "gs_pop_get_count_fast", "title": "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", "topics": [ "getPopStats,GatingSet-method", "gs_pop_get_count_fast", "gs_pop_get_count_with_meta" ] }, { "page": "gs_pop_get_gate", "title": "Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet.", "topics": [ "getGate", "getGate,GatingHierarchy,character-method", "getGate,GatingSet,character-method", "getGate,GatingSetList,character-method", "gh_pop_get_gate", "gs_pop_get_gate" ] }, { "page": "gs_pop_get_gs", "title": "subset gs by population node", "topics": [ "gs_pop_get_gs" ] }, { "page": "gs_pop_get_children", "title": "Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy", "topics": [ "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" ] }, { "page": "gs_pop_get_stats", "title": "Extract stats from populations(or nodes)", "topics": [ "getStats", "getStats,GatingHierarchy-method", "getStats,GatingSet-method", "getStats,GatingSetList-method", "gh_pop_get_stats", "gs_pop_get_stats" ] }, { "page": "gs_pop_get_stats_tfilter", "title": "Extract stats from populations(or nodes) within a restricted time window", "topics": [ "gh_pop_get_stats_tfilter", "gs_pop_get_stats_tfilter" ] }, { "page": "gs_pop_set_gate", "title": "update the gate", "topics": [ "gh_pop_set_gate", "gs_pop_set_gate", "setGate", "setGate,GatingHierarchy,character,filter-method", "setGate,GatingSet,character,ANY-method" ] }, { "page": "gs_pop_set_name", "title": "Update the name of one node in a gating hierarchy/GatingSet.", "topics": [ "gh_pop_set_name", "gs_pop_set_name", "setNode", "setNode,GatingHierarchy,character,ANY-method", "setNode,GatingHierarchy,character,character-method", "setNode,GatingSet,character,ANY-method" ] }, { "page": "gs_pop_set_visibility", "title": "hide/unhide a node", "topics": [ "gh_pop_set_visibility", "gs_pop_set_visibility", "setNode,GatingHierarchy,character,logical-method" ] }, { "page": "gs_remove_redundant_channels", "title": "Remove the channels from flow data that are not used by gates", "topics": [ "dropRedundantChannels", "gs_remove_redundant_channels" ] }, { "page": "gs_remove_redundant_nodes", "title": "Remove the terminal leaf nodes that make the gating trees to be different from one another.", "topics": [ "dropRedundantNodes", "gs_remove_redundant_nodes" ] }, { "page": "gs_split_by_channels", "title": "split GatingSets into groups based on their flow channels", "topics": [ "groupByChannels", "gs_split_by_channels" ] }, { "page": "gs_split_by_tree", "title": "split GatingSets into groups based on their gating schemes Be careful that the splitted resluts still points to the original data set!!", "topics": [ "groupByTree", "gs_split_by_tree" ] }, { "page": "gs_update_channels", "title": "Update the channel information of a GatingSet (c++ part)", "topics": [ "gs_update_channels", "updateChannels" ] }, { "page": "gslist_to_gs", "title": "Merge a GatingSetList into a single GatingSet", "topics": [ "gslist_to_gs", "rbind2,GatingSetList,missing-method" ] }, { "page": "identifier-methods", "title": "Retrieve/replace the GUID of a GatingSet or GatingSetList", "topics": [ "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" ] }, { "page": "keyword", "title": "Retrieve a specific keyword for a specific sample in a 'GatingHierarchy' or or set of samples in a 'GatingSet' or 'GatingSetList'", "topics": [ "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" ] }, { "page": "keyword-mutators", "title": "Methods to alter keywords in 'cytoframe', 'cytoset', 'GatingHierarchy', or 'GatingSet' objects", "topics": [ "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" ] }, { "page": "lapply-methods", "title": "apply 'FUN' to each sample (i.e. 'GatingHierarchy' or 'cytoframe') in a 'GatingSet' or 'cytoset'", "topics": [ "lapply", "lapply,cytoset-method", "lapply,GatingSet-method", "lapply-methods" ] }, { "page": "length", "title": "Methods to get the length of a GatingSet", "topics": [ "length", "length,GatingSet-method", "show,GatingSet-method" ] }, { "page": "load_cytoframe", "title": "Load the cytoframe from disk", "concept": [ "cytoframe/cytoset IO functions" ], "topics": [ "load_cytoframe" ] }, { "page": "load_cytoframe_from_fcs", "title": "Read a single FCS file in to a cytoframe", "concept": [ "cytoframe/cytoset IO functions" ], "topics": [ "load_cytoframe_from_fcs" ] }, { "page": "load_cytoset_from_fcs", "title": "Read one or several FCS files in to a cytoset", "concept": [ "cytoframe/cytoset IO functions" ], "topics": [ "load_cytoset_from_fcs" ] }, { "page": "load_meta", "title": "Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe)", "topics": [ "cf_flush_meta", "cf_load_meta", "cs_flush_meta", "cs_load_meta", "flush_meta", "load_meta" ] }, { "page": "lock", "title": "Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag", "topics": [ "cf_lock", "cf_unlock", "cs_lock", "cs_unlock", "lock" ] }, { "page": "logicle_trans", "title": "logicle transformation.", "topics": [ "logicle_trans" ] }, { "page": "logicleGml2_trans", "title": "GatingML2 version of logicle transformation.", "topics": [ "logicleGml2_trans" ] }, { "page": "logtGml2_trans", "title": "Gating-ML 2.0 Log transformation.", "topics": [ "logtGml2_trans" ] }, { "page": "markernames", "title": "Get/set the column(channel) or marker names", "topics": [ "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" ] }, { "page": "merge_list_to_gs", "title": "Merge a list of GatingSets into a single GatingSet", "topics": [ "merge_list_to_gs" ] }, { "page": "ncFlowSet-methods", "title": "Fetch the flowData object associated with a GatingSet .", "topics": [ "ncFlowSet", "ncFlowSet,GatingSet-method", "ncFlowSet<-", "ncFlowSet<-,GatingSet-method" ] }, { "page": "nodeflags", "title": "The flags of gate nodes", "topics": [ "gh_pop_is_bool_gate", "gh_pop_is_gated", "gh_pop_is_hidden", "gh_pop_is_negated", "isGated", "isHidden", "isNegated", "nodeflags" ] }, { "page": "openWorkspace", "title": "It is now moved along with entire flowJo parser to CytoML package", "topics": [ "openWorkspace" ] }, { "page": "pData-methods", "title": "read/set pData of flow data associated with 'GatingHierarchy', 'GatingSet', or 'GatingSetList'", "topics": [ "pData", "pData,GatingHierarchy-method", "pData,GatingSet-method", "pData-methods", "pData<-", "pData<-,GatingSet,data.frame-method", "pData<-,GatingSetList,data.frame-method" ] }, { "page": "plot-methods", "title": "plot a gating tree", "topics": [ "plot", "plot,GatingSet,character-method", "plot,GatingSet,missing-method", "plot-methods" ] }, { "page": "pop_add", "title": "Add populations to a GatingHierarchy", "topics": [ "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" ] }, { "page": "prettyAxis", "title": "Determine tick mark locations and labels for a given channel axis", "topics": [ "prettyAxis" ] }, { "page": "recompute", "title": "Compute the cell events by the gates stored within the gating tree.", "topics": [ "recompute", "recompute.GatingSet", "recompute.GatingSetList" ] }, { "page": "rotate_gate", "title": "Simplified geometric rotation of gates associated with nodes", "topics": [ "rotate_gate", "rotate_gate,GatingHierarchy-method", "rotate_gate,GatingSet-method", "rotate_gate.GatingHierarchy" ] }, { "page": "sampleNames", "title": "Get/update sample names in a GatingSet", "topics": [ "sampleNames", "sampleNames,cytoset,", "sampleNames,cytoset-method", "sampleNames,GatingSet-method", "sampleNames<-", "sampleNames<-,GatingSet,ANY-method", "sampleNames<-,GatingSet-method" ] }, { "page": "save_cytoset", "title": "save/load a cytoset to/from disk.", "topics": [ "load_cytoset", "save_cytoset" ] }, { "page": "save_gs", "title": "save/load a GatingSet/GatingSetList to/from disk.", "topics": [ "load_gs", "load_gslist", "sampleNames,character-method", "save_gs", "save_gslist" ] }, { "page": "scale_gate", "title": "Simplified geometric scaling of gates associated with nodes", "topics": [ "scale_gate", "scale_gate,GatingHierarchy-method", "scale_gate,GatingSet-method", "scale_gate.GatingHierarchy" ] }, { "page": "shift_gate", "title": "Simplified geometric translation of gates associated with nodes", "topics": [ "shift_gate", "shift_gate,GatingHierarchy-method", "shift_gate,GatingSet-method", "shift_gate.GatingHierarchy" ] }, { "page": "standardize-GatingSet", "title": "The tools to standardize the tree structures and channel names.", "topics": [ "merge-GatingSet", "standardize-GatingSet" ] }, { "page": "stats.fun", "title": "built-in stats functions.", "topics": [ "pop.MFI", "stats.fun" ] }, { "page": "subset", "title": "subset the GatingSet/GatingSetList based on 'pData'", "topics": [ "subset", "subset.GatingSet" ] }, { "page": "swap_data_cols", "title": "Swap the colnames Perform some validity checks before returning the updated colnames", "topics": [ "swap_data_cols" ] }, { "page": "transform", "title": "tranform the flow data asssociated with the GatingSet", "topics": [ "transform", "transform,GatingSet-method", "transform,GatingSetList-method" ] }, { "page": "transform_gate", "title": "Simplified geometric transformations of gates associated with nodes", "topics": [ "transform_gate", "transform_gate,GatingHierarchy-method", "transform_gate,GatingSet-method", "transform_gate.GatingHierarchy" ] }, { "page": "transformerList", "title": "Constructor for transformerList object", "topics": [ "transformerList" ] } ], "_pkglogo": "https://github.com/bioc/flowWorkspace/raw/HEAD/logo.png", "_readme": "https://github.com/bioc/flowWorkspace/raw/HEAD/README.md", "_rundeps": [ "abind", "BH", "Biobase", "BiocGenerics", "biocmake", "cli", "cpp11", "cytolib", "data.table", "DelayedArray", "dir.expiry", "dplyr", "farver", "filelock", "flowCore", "generics", "ggplot2", "glue", "graph", "gtable", "IRanges", "isoband", "labeling", "lattice", "lifecycle", "magrittr", "Matrix", "MatrixGenerics", "matrixStats", "ncdfFlow", "pillar", "pkgconfig", "R6", "RBGL", "RColorBrewer", "Rcpp", "Rgraphviz", "Rhdf5lib", "rlang", "RProtoBufLib", "S4Arrays", "S4Vectors", "S7", "scales", "SparseArray", "tibble", "tidyselect", "utf8", "vctrs", "viridisLite", "withr", "XML", "XVector" ], "_sysdeps": [ { "shlib": "libcurl", "package": "libcurl4t64", "headers": "libcurl4-openssl-dev", "source": "curl", "version": "8.5.0-2ubuntu10.9", "name": "curl", "homepage": 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"homepage": "http://gcc.gnu.org/", "description": "GNU Standard C++ Library v3" } ], "_vignettes": [ { "source": "flowWorkspace-Introduction.Rmd", "filename": "flowWorkspace-Introduction.html", "title": "flowWorkspace Introduction: A Package to store and maninpulate gated flow data", "author": "Greg Finak greg@ozette.ai, Mike Jiang mike@ozette.ai", "engine": "knitr::rmarkdown", "headings": [ "Purpose", "Basics on GatingSet", "GatingHierarchy", "Build the GatingSet from scratch", "Archive and Clone", "The cytoframe and cytoset classes", "Reading a cytoframe", "cytoframe Accessors", "Pass By Reference", "Views", "Deep Copy", "Interconversion between cytoframe and flowFrame", "Saving/Loading a cytoframe in h5", "cytoset methods", "Troubleshooting and error reporting" ], "created": "2016-02-05 00:37:49", "modified": "2024-01-17 02:57:21", "commits": 22 }, { "source": "HowToMergeGatingSet.Rmd", "filename": "HowToMergeGatingSet.html", "title": "How to merge/standardize GatingSets", "author": 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