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

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

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 #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+") }