gs_pop_add: Create a GatingSet and add/remove the flowCore gate(or...

In flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Description

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.

Usage

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

gs_pop_remove(gs, node, ...)

Arguments

gs	A GatingSet
gate	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.
validityCheck	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.
node	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.

See Also

GatingSet-class

Examples

## Not run: 
    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
    
#add one gate
    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 
    
#add a quadGate
    qg <- quadGate("FL1-H"=2, "FL2-H"=4)
    nodeIDs<-gs_pop_add(gs,qg,parent="rectangle")
    nodeIDs #quadGate produces four population nodes
    gs_get_pop_paths(gs[[1]]) #population names are named after dimensions of gate if not specified
    
#add a boolean Gate
    bg<-booleanFilter(`CD15 FITC-CD45 PE+|CD15 FITC+CD45 PE-`)
    bg
    nodeID2<-gs_pop_add(gs,bg,parent="rectangle")
    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]])
    
    #add logical vectors as gate
    lg <- sapply(sampleNames(gs), function(sn){
                                   gh <- gs[[sn]]
                                   dat <- exprs(gh_pop_get_data(gh, "cd3+"))#get events data matrix for this sample at cd3+ node
                                   vec <- dat[, "FSC-A"] > 1e4 & data[, "SSC-A"] > 1e5
                                   vec
                                   })
   gs_pop_add(gs, lg, name = "new_bool", parent = "cd3+")
 
## End(Not run)

flowWorkspace documentation built on Nov. 8, 2020, 8:08 p.m.