directly update event indices without changing gates

Description

It is useful when we want to alter the popluation at events level yet without removing or adding the existing gates.

Usage

## S4 method for signature 'GatingHierarchy,character,logical'
updateIndices(obj, y, z)

Arguments

Examples

library(flowWorkspace)
dataDir <- system.file("extdata",package="flowWorkspaceData")
suppressMessages(gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE)))
gh <- gs[[1]]
#get pop counts
pop.stats <- getStats(gh, nodes = c("CD3+", "CD4", "CD8"))
pop.stats

# subsample 30% cell events at CD3+ node
total.cd3 <- pop.stats[pop == "CD3+", count]
gInd <- seq_len(total.cd3) #create integer index for cd3
gInd <- sample.int(total.cd3, size = total.cd3 * 0.3) #randomly select 30%
#convert it to logicle index
gInd.logical <- rep(FALSE, total.cd3)
gInd.logical[gInd] <- TRUE
#replace the original index stored at GatingHierarchy
updateIndices(gh, "CD3+", gInd.logical)
#check the updated pop counts
getStats(gs[[1]], nodes = c("CD3+", "CD4", "CD8")) #note that CD4, CD8 are not updated
#update all the descendants of CD3+
nodes <- getDescendants(gh, "CD3+")
for (node in nodes) suppressMessages(recompute(gh, node))
getStats(gs[[1]], nodes = c("CD3+", "CD4", "CD8")) #now all are update to date