GatingSet method creates a gatingset from a flowSet with the ungated data as the root node. add method add the flowCore gate to a GatingHierarchy/GatingSet. gs_pop_set_gate method update the gate of one population node in GatingHierarchy/GatingSet. Rm method Remove the population node from a GatingHierarchy/GatingSet. They are equivalent to the workFlow,add and Rm methods in flowCore package. recompute method does the actual gating after the gate is added,i.e. calculating the event indices according to the gate definition.

gs_pop_add(gs, gate, validityCheck = TRUE, ...)

gs_pop_remove(gs, node, ...)

## Arguments

gs A GatingSet A flowCore::filter or a list of flowCore::filters or logical vectors to be added to the GatingSet. when logical vectors, they represent the indices of events to be included in the populations. It can be global that represents the index to the original full events or local index that is relative to the parent population cell events. See examples for more details. logical whether to check the consistency of tree structure across samples. default is TRUE. Can be turned off when speed is prefered to the robustness. some other arguments to specify how the gates are added to the gating tree. names a character vector of length four,which specifies the population names resulted by adding a quadGate.The order of the names is clock-wise starting from the top left quadrant population. parent a character scalar to specify the parent node name where the new gate to be added to, by default it is NULL,which indicates the root node name a character scalar to specify the node name of population that is generated by the gate to be added. recompute a logical flag negated: a logical scalar to specify whether the gate is negated,which means the the population outside of the gate will be kept as the result population. It is FALSE by default. A character identifies the population node in a GatingHierrarchy or GatingSet to remove

## Value

GatingSet method returns a GatingSet object with just root node. add method returns a population node ID (or four population node IDs when adding a quadGate) that uniquely identify the population node within a GatingHierarchy.

GatingSet-class

## Examples

if (FALSE) {
library(flowCore)
data(GvHD)
#select raw flow data
fs<-GvHD[1:3]

#transform the raw data
tf <- transformList(colnames(fs[[1]])[3:6], asinh, transformationId="asinh")
fs_trans<-transform(fs,tf)

#add transformed data to a gatingset
gs <- GatingSet(fs_trans)
gs
gs_get_pop_paths(gs[[1]]) #only contains root node

rg <- rectangleGate("FSC-H"=c(200,400), "SSC-H"=c(250, 400),
filterId="rectangle")

nodeID<-gs_pop_add(gs, rg)#it is added to root node by default if parent is not specified
nodeID
gs_get_pop_paths(gs[[1]]) #the second population is named after filterId of the gate

nodeIDs #quadGate produces four population nodes
gs_get_pop_paths(gs[[1]]) #population names are named after dimensions of gate if not specified

bg<-booleanFilter(CD15 FITC-CD45 PE+|CD15 FITC+CD45 PE-)
bg
nodeID2
gs_get_pop_paths(gs[[1]])
#do the actual gating
recompute(gs)

#plot one gate for one sample
autoplot(gs[[1]],"rectangle")
autoplot(gs[[1]],nodeIDs) #may be smoothed automatically if there are not enough events after gating

#plot gates across samples using lattice plot
autoplot(gs,nodeID)
#plot all gates for one sample
autoplot(gs[[1]])#boolean gate is skipped by default
autoplot(gs[[1]],bool=TRUE)

#plot the gating hierarchy
plot(gs[[1]])
#remove one node causing the removal of all the descendants
gs_pop_remove('rectangle', gs = gs)
gs_get_pop_paths(gs[[1]])