| 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 |
| 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!! |
| 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. |
| 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 |