GatingHierarchy and GatingSet classesClasses for managing compensation, transformation, and gating of cytometry data (FCS files) and methods for creating them |
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Class GatingHierarchy |
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constructors for GatingSet |
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Bracket operators on |
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Retrieve/replace the GUID of a GatingSet or GatingSetList |
convert the legacy GatingSet archive (mixed with R and C++ files) to the new format (C++ only) |
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cytoframe and cytoset classesReference classes for efficiently managing the representation of data from FCS files (analagous to flowFrame and flowSet classes from the flowCore package) |
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Methods for conversion between flowCore and flowWorkspace data classes |
Read a single FCS file in to a cytoframe |
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Return the file path of the underlying h5 file |
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Save the cytoframe as h5 format |
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Read one or several FCS files in to a cytoset |
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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) |
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Add a cytoframe to a cytoset |
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update a cytoframe in a cytoset |
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Return the path of the underlying data files |
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Flush/load meta data (keywords, pData, channels/markers) to/from disk (only valid for on-disk cytoset/cytoframe) |
Lock/Unlock the cytoset/cytoframe by turning on/off its read-only flag |
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Append data columns to a flowFrame |
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Methods to change channel and marker names for |
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Methods to alter keywords in |
Examining the hierarchical gating treeFunctions for examining the subpopulations resulting from applying gates to the data |
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plot a gating tree |
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visualize the tree structure differnece among the GatingSets |
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Get the names of all nodes from a gating hierarchy. |
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get all the leaf nodes |
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try to determine the redundant terminal(or leaf) nodes that can be removed |
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Remove the terminal leaf nodes that make the gating trees to be different from one another. |
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Retrieve the cluster labels from the cluster nodes |
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check if a node is clustering node |
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Extract the population name from the node path It strips the parent path and cluster method name. |
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convert the partial gating path to the full path |
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Return the name of the parent population or a list of child populations of the current population in the GatingHierarchy |
get all the descendant nodes for the given ancester |
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Extract stats from populations(or nodes) |
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Extract stats from populations(or nodes) within a restricted time window |
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Compare the stats(count/freq) between the version parsed from xml and the one recalculated/gated from R |
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Plot the coefficient of variation between xml and openCyto population statistics for each population in a gating hierarchy. |
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Get count or proportion from populations |
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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 |
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Accessing underyling dataFunctions for accessing or altering the flowFrame or flowSet objects underlying the gating analysis. These can also be useful in preparing GatingSet objects for merging. |
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determine whether the flow data associated with a GatingSet is persistent(on-disk) or in-memory |
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Fetch or replace the flowData object associated with a GatingSet . |
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get gated flow data from a GatingHierarchy/GatingSet/GatingSetList |
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Retrieve the compensation matrices from a |
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extract compensation object from GatingSet |
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Return a list of transformations or a transformation in a GatingHierarchy |
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compensate the flow data asssociated with the GatingSet |
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tranform the flow data asssociated with the GatingSet |
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Methods to get the length of a GatingSet |
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Get/update sample names in a GatingSet |
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Get/set the column(channel) or marker names |
read/set pData of flow data associated with |
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Retrieve a specific keyword for a specific sample in a |
Perform gating analysisFunctions for accessing, altering, adding, and removing gate definitions and their resulting subpopulations. These can also be useful in preparing GatingSet objects for merging. |
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The flags of gate nodes |
hide/unhide a node |
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save the event counts parsed from xml into c++ tree structure |
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Return the flowCore gate definition associated with a node in a GatingHierarchy/GatingSet. |
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update the gate |
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Compute the cell events by the gates stored within the gating tree. |
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Update the name of one node in a gating hierarchy/GatingSet. |
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Simplified geometric transformations of gates associated with nodes |
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Simplified geometric rotation of gates associated with nodes |
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Simplified geometric scaling of gates associated with nodes |
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Simplified geometric translation of gates associated with nodes |
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subset the GatingSet/GatingSetList based on 'pData' |
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Get the membership indices for each event with respect to a particular gate in a GatingHierarchy |
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Return the single-cell matrix of 1/0 dichotomized expression |
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directly update event indices without changing gates |
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Return the cell events data that express in any of the single populations defined in |
built-in stats functions. |
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Add populations to a GatingHierarchy |
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Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet. |
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move a node along with all of its descendant nodes to the given ancester |
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Copy a node along with all of its descendant nodes to the given ancestor |
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Construct a |
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The tools to standardize the tree structures and channel names. |
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Update the channel information of a GatingSet (c++ part) |
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Remove the channels from flow data that are not used by gates |
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split GatingSets into groups based on their flow channels |
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split GatingSets into groups based on their gating schemes Be careful that the splitted resluts still points to the original data set!! |
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Merge a list of GatingSets into a single GatingSet |
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apply |
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Merge a GatingSetList into a single GatingSet |
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Helpers to generate transformations and filtersFunctions for quickly constructing transformations or filters or converting them to a form that can be applied to data in a GatingHierachy or GatingSet |
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helper function to generate a trans objects Used by other specific trans constructor |
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Constructor for transformerList object |
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Compute logicle transformation from the flowData associated with a GatingHierarchy |
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convert flowCore filter to a list It convert the flowCore gate to a list whose structure can be understood by underlying c++ data structure. |
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inverse hyperbolic sine transform function generator (GatingML 2.0 version) |
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Inverse hyperbolic sine transformation. |
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logicle transformation. |
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GatingML2 version of logicle transformation. |
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Gating-ML 2.0 Log transformation. |
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inverse hyperbolic sine transform function |
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flowJo inverse hyperbolic sine transformation. |
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flog transform function |
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construct the flowJo-type biexponentioal transformation function |
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flowJo biexponential transformation. |
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A class describing logical operation (& or |) of the reference populations |
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Read/write GatingSet objectsFunctions to read save GatingSet objects to disk or read them in to an R session |
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save/load a GatingSet/GatingSetList to/from disk. |
Plotting functionsMethods for plotting the hierarchical gating tree and gates. More dedicated plotting methods for GatingSet and GatingHierarchy objects are provided by the ggcyto package, |
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plot a gating tree |
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Plot gates and associated cell population contained in a |
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Determine tick mark locations and labels for a given channel axis |
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Miscellaneous helper functionsFunctions whose role does not easily fit in to one of the above categories |
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get/set the log level |
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Generate the breaks that makes sense for flow data visualization |
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Swap the colnames Perform some validity checks before returning the updated colnames |
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Remove temporary files associatated with flowWorkspace data classes |