add,GatingSet,list-method {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.
setGate
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.
## S4 method for signature 'GatingSet,list' add(wf, action, ...) ## S4 method for signature 'GatingSetList,list' add(wf, action, ...) ## S4 method for signature 'GatingSet,filtersList' add(wf, action, ...) ## S4 method for signature 'GatingSet,filterList' add(wf, action, validityCheck = TRUE, ...) ## S4 method for signature 'GatingSetList,filterList' add(wf, action, ...) ## S4 method for signature 'GatingSetList,filtersList' add(wf, action, ...) ## S4 method for signature 'GatingSet,filter' add(wf, action, ...) ## S4 method for signature 'GatingSet,filters' add(wf, action, ...) ## S4 method for signature 'GatingSetList,filter' add(wf, action, ...) ## S4 method for signature 'GatingSetList,filters' add(wf, action, ...) ## S4 method for signature 'GatingHierarchy,filter' add(wf, action, ...) ## S4 method for signature 'GatingHierarchy,filters' add(wf, action, names = NULL, ...) ## S4 method for signature 'GatingHierarchy,quadGate' add(wf, action, names = NULL, ...) ## S4 method for signature 'GatingHierarchy,logical' add(wf, action, parent, name, recompute, ...) ## S4 method for signature 'GatingHierarchy,factor' add(wf, action, name = NULL, ...) ## S4 method for signature 'GatingHierarchy,logicalFilterResult' add(wf, action, ...) ## S4 method for signature 'GatingHierarchy,multipleFilterResult' add(wf, action, name = NULL, ...) ## S4 method for signature 'character,GatingSet,character' Rm(symbol, envir, subSymbol, ...) ## S4 method for signature 'character,GatingSetList,character' Rm(symbol, envir, subSymbol, ...) ## S4 method for signature 'character,GatingHierarchy,character' Rm(symbol, envir, subSymbol, ...)
wf |
A |
action |
A |
... |
some other arguments to specify how the gates are added to the gating tree.
|
validityCheck |
|
names |
a |
parent |
a |
name |
a |
recompute |
a |
symbol |
A |
envir |
A |
subSymbol |
Not used. |
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: 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 getNodes(gs[[1]]) #only contains root node #add one gate rg <- rectangleGate("FSC-H"=c(200,400), "SSC-H"=c(250, 400), filterId="rectangle") nodeID<-add(gs, rg)#it is added to root node by default if parent is not specified nodeID getNodes(gs[[1]]) #the second population is named after filterId of the gate #add a quadGate qg <- quadGate("FL1-H"=2, "FL2-H"=4) nodeIDs<-add(gs,qg,parent="rectangle") nodeIDs #quadGate produces four population nodes getNodes(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<-add(gs,bg,parent="rectangle") nodeID2 getNodes(gs[[1]]) #do the actual gating recompute(gs) #plot one gate for one sample plotGate(gs[[1]],"rectangle") plotGate(gs[[1]],nodeIDs) #may be smoothed automatically if there are not enough events after gating #plot gates across samples using lattice plot plotGate(gs,nodeID) #plot all gates for one sample plotGate(gs[[1]])#boolean gate is skipped by default plotGate(gs[[1]],bool=TRUE) #plot the gating hierarchy require(Rgraphviz) plot(gs[[1]]) #remove one node causing the removal of all the descendants Rm('rectangle', gs) getNodes(gs[[1]]) ## End(Not run)