R/merge.quad.gates.R
merge.quad.gates.Rd
For internal usage.
# S3 method for quad.gates merge(gh, pops, bool = TRUE)
gh | a GatingHierarchy |
---|---|
pops | a vector of population names |
bool | whether to deal with boolean gate |
a nested list of data structure that captures the information of parent, grouped populations (with the same projections) and the reconstructed quadGate object and the respective quadrant pattern
library(flowWorkspace) dataDir <- system.file("extdata",package="flowWorkspaceData") gs <- load_gs(file.path(dataDir, "gs_manual")) #get the GatingHierarchy object gh <- gs[[1]] pops <- gs_pop_get_children(gh, "CD4") grps <- ggcyto:::merge.quad.gates(gh, pops) length(grps) # pops are grouped into two#> [1] 2grps[[1]] # each group is annotaed with quadGate information#> $popIds #> $popIds$quad.gate #> Quadrant gate 'defaultQuadGate' with dimensions: #> <R660-A>: 1892.233 #> <V545-A>: 1968.89 #> #> $popIds$quad.pattern #> [1] "-+" "++" "+-" "--" #> #> $popIds$pop.name #> [1] "/not debris/singlets/CD3+/CD4/38- DR+" #> [2] "/not debris/singlets/CD3+/CD4/38+ DR+" #> [3] "/not debris/singlets/CD3+/CD4/38+ DR-" #> [4] "/not debris/singlets/CD3+/CD4/38- DR-" #> #> #> $parentId #> [1] "CD4" #>ggcyto:::merge.quad.gates(gh, gs_pop_get_children(gh, "CD3+")) # cd3 subsets are not coercible to quadgate thus return as they are#> $`/not debris/singlets/CD3+/CD4` #> $`/not debris/singlets/CD3+/CD4`$popIds #> [1] "/not debris/singlets/CD3+/CD4" "/not debris/singlets/CD3+/CD8" #> [3] "/not debris/singlets/CD3+/DNT" "/not debris/singlets/CD3+/DPT" #> #> $`/not debris/singlets/CD3+/CD4`$parentId #> [1] "CD3+" #> #>