gs_pop_add {flowWorkspace} | R Documentation |
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, ...)
gs |
A |
gate |
A |
validityCheck |
|
... |
some other arguments to specify how the gates are added to the gating tree.
|
node |
A |
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
.
## 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)