# Infrastructure for representing and interacting with gated and ungated cytometry data sets.

## Documentation for package ‘flowWorkspace’ version 3.32.0

- DESCRIPTION file.
- User guides, package vignettes and other documentation.
- Package NEWS.

## Help Pages

A B C D E F G I K L M N O P R S T U misc

flowWorkspace-package | Import and replicate flowJo workspaces and gating schemes using flowCore.

## -- A --

add | Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
add-method | Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
asinhtGml2_trans | Inverse hyperbolic sine transformation.
asinh_Gml2 | inverse hyperbolic sine transform function generator (GatingML 2.0 version)

## -- B --

booleanFilter | A class describing logical operation (& or |) of the reference populations
booleanFilter-class | A class describing logical operation (& or |) of the reference populations

## -- C --

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
clone | clone a GatingSet
clone-method | clone a GatingSet
clone-methods | clone a GatingSet
colnames-method | Get/set the column(channel) or marker names
colnames<--method | Get/set the column(channel) or marker names
compensate-method | compensate the flow data asssociated with the GatingSet
compute_timestep | compute time step from fcs keyword
copyNode | Copy a node along with all of its descendant nodes to the given ancestor

## -- D --

dropRedundantChannels | Remove the channels from flow data that are not used by gates
dropRedundantNodes | Remove the terminal leaf nodes that make the gating trees to be different from one another.

## -- E --

estimateLogicle.GatingHierarchy | Compute logicle transformation from the flowData associated with a GatingHierarchy
extract_cluster_pop_name_from_node | Extract the population name from the node path It strips the parent path and cluster method name.

## -- F --

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.
fix_channel_slash | toggle the channel names between '/' and '_' character
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 .
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_trans | flowJo biexponential transformation.
flowJo_fasinh_trans | flowJo inverse hyperbolic sine transformation.
flowWorkspace | Import and replicate flowJo workspaces and gating schemes using flowCore.
flowWorkspace.par.get | flowWorkspace.par.set sets a set of parameters in the flowWorkspace package namespace.
flowWorkspace.par.init | workspace version is parsed from xml node '/Workspace/version' in flowJo workspace and matched with this list to dispatch to the one of the three workspace parsers
flowWorkspace.par.set | flowWorkspace.par.set sets a set of parameters in the flowWorkspace package namespace.
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

## -- G --

GatingHierarchy-class | Class GatingHierarchy
GatingSet | Class '"GatingSet"'
GatingSet-class | Class '"GatingSet"'
GatingSet-method | 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
getCompensationMatrices.GatingHierarchy | Retrieve the compensation matrices from a GatingHierarchy
getCompensationObj | extract compensation object from 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
getFullNodePath | convert the partial gating path to the full path
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.
getIndiceMat | Return the single-cell matrix of 1/0 dichotomized expression
getIndices | Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
getIndices-method | routine to return the indices by specify boolean combination of reference nodes:
getIndices-method | Get the membership indices for each event with respect to a particular gate in a GatingHierarchy
getLoglevel | get/set the log level
getMergedStats | Get Cell Population Statistics and Sample Metadata
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 | 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-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 | 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-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
getSingleCellExpression | Return the cell events data that express in any of the single populations defined in 'y'
getSingleCellExpression-method | 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 | Exact MFI from populations(or nodes) for all the markers
getStats.GatingHierarchy | Exact MFI from populations(or nodes) for all the markers
getStats.GatingSet | Exact MFI from populations(or nodes) for all the markers
getStats.GatingSetList | Exact MFI from populations(or nodes) for all the markers
getTotal | 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
getTotal-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
getTransformations | Return a list of transformations or a transformation in a GatingHierarchy
getTransformations.GatingHierarchy | Return a list of transformations or a transformation in a GatingHierarchy
get_leaf_nodes | get all the leaf nodes
gh_check_cluster_node | check if a node is clustering node
gh_get_cluster_labels | Retrieve the cluster labels from the cluster nodes
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!!

## -- I --

identifier-method | constructors for GatingSet
identifier<--method | constructors for GatingSet
insertGate | insert a dummy gate to the GatingSet
isGated | The flags of gate nodes isGated checks if a node is already gated isNegated checks if a node is negated. isHidden checks if a node is hidden.
isGated-method | The flags of gate nodes isGated checks if a node is already gated isNegated checks if a node is negated. isHidden checks if a node is hidden.
isHidden | The flags of gate nodes isGated checks if a node is already gated isNegated checks if a node is negated. isHidden checks if a node is hidden.
isHidden-method | The flags of gate nodes isGated checks if a node is already gated isNegated checks if a node is negated. isHidden checks if a node is hidden.
isNcdf | determine the flow data associated with a Gating Hiearchy is based on 'ncdfFlowSet' or 'flowSet'
isNegated | The flags of gate nodes isGated checks if a node is already gated isNegated checks if a node is negated. isHidden checks if a node is hidden.
isNegated-method | The flags of gate nodes isGated checks if a node is already gated isNegated checks if a node is negated. isHidden checks if a node is hidden.

## -- K --

keyword | Retrieve a specific keyword for a specific sample in a 'GatingHierarchy' or or set of samples in a 'GatingSet' or 'GatingSetList'
keyword-method | Retrieve a specific keyword for a specific sample in a 'GatingHierarchy' or or set of samples in a 'GatingSet' or 'GatingSetList'

## -- L --

lapply-method | apply 'FUN' to each sample (i.e. 'GatingHierarchy')
length | Methods to get the length of a GatingSet
length-method | Methods to get the length of a GatingSet
load_gs | save/load a GatingSet/GatingSetList to/from disk.
load_gslist | save/load a GatingSet/GatingSetList to/from disk.
logicleGml2_trans | GatingML2 version of logicle transformation.
logicle_trans | logicle transformation.
logtGml2_trans | Gating-ML 2.0 Log transformation.

## -- M --

markernames-method | Get/set the column(channel) or marker names
markernames<--method | Get/set the column(channel) or marker names
merge-GatingSet | The tools to standardize the tree structures and channel names.
mkformula | make a formula from a character vector
moveNode | move a node along with all of its descendant nodes to the given ancester

## -- N --

ncFlowSet | Fetch the flowData object associated with a GatingSet .
ncFlowSet-method | Fetch the flowData object associated with a GatingSet .
ncFlowSet<- | Fetch the flowData object associated with a GatingSet .
ncFlowSet<--method | Fetch the flowData object associated with a GatingSet .

## -- O --

openWorkspace | It is now moved along with entire flowJo parser to CytoML package
openWorkspace.default | It is now moved along with entire flowJo parser to CytoML package

## -- P --

pData | read/set pData of flow data associated with 'GatingSet' or 'GatingSetList'
pData-method | read/set pData of flow data associated with 'GatingSet' or 'GatingSetList'
pData<- | read/set pData of flow data associated with 'GatingSet' or 'GatingSetList'
pData<--method | read/set pData of flow data associated with 'GatingSet' or 'GatingSetList'
plot | plot a gating tree
plot-method | plot a gating tree
plotGate | Plot gates and associated cell population contained in a 'GatingHierarchy' or 'GatingSet'
plotGate-method | Plot gates and associated cell population contained in a 'GatingHierarchy' or 'GatingSet'
plotGate-methods | Plot gates and associated cell population contained in a 'GatingHierarchy' or 'GatingSet'
plotPopCV | Plot the coefficient of variation between xml and openCyto population statistics for each population in a gating hierarchy.
plotPopCV-method | Plot the coefficient of variation between xml and openCyto population statistics for each population in a gating hierarchy.
plot_diff_tree | visualize the tree structure differnece among the GatingSets
pop.MFI | built-in stats functions.
prettyAxis | Determine tick mark locations and labels for a given channel axis

## -- R --

rbind2-method | Class '"GatingSetList"'
recompute | Compute the cell events by the gates stored within the gating tree.
recompute-method | Compute the cell events by the gates stored within the gating tree.
Rm | Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
Rm-method | Create a GatingSet and add/remove the flowCore gate(or population) to/from a GatingHierarchy/GatingSet.
rotate_gate | Simplified geometric rotation of gates associated with nodes
rotate_gate.GatingHierarchy | Simplified geometric rotation of gates associated with nodes
rotate_gate.GatingSet | Simplified geometric rotation of gates associated with nodes

## -- S --

sampleNames | Get/update sample names in a GatingSet
sampleNames-method | Get/update sample names in a GatingSet
sampleNames<- | Get/update sample names in a GatingSet
sampleNames<--method | Get/update sample names in a GatingSet
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.GatingHierarchy | Simplified geometric scaling of gates associated with nodes
scale_gate.GatingSet | Simplified geometric scaling of gates associated with nodes
set.count.xml | save the event counts parsed from xml into c++ tree structure
setGate | update the gate
setGate-method | update the gate
setLoglevel | get/set the log level
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.
shift_gate | Simplified geometric translation of gates associated with nodes
shift_gate.GatingHierarchy | Simplified geometric translation of gates associated with nodes
shift_gate.GatingSet | 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 | Methods to get the length of a GatingSet
standardize-GatingSet | The tools to standardize the tree structures and channel names.
subset.GatingSet | subset the GatingSet/GatingSetList based on 'pData'
swap_data_cols | Swap the colnames Perform some validity checks before returning the updated colnames

## -- T --

transform-method | tranform the flow data asssociated with the GatingSet
transformerList | Constructor for transformerList object
transform_gate | Simplified geometric transformations of gates associated with nodes
transform_gate.GatingHierarchy | Simplified geometric transformations of gates associated with nodes

## -- U --

updateChannels | Update the channel information of a GatingSet (c++ part)
updateIndices-method | directly update event indices without changing gates

## -- misc --

[-method | Class '"GatingSet"'
[[-method | Class '"GatingSet"'