gh_pop_set_indices: directly update event indices without changing gates

In flowWorkspace: Infrastructure for representing and interacting with gated and ungated cytometry data sets.

Description

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

Usage

gh_pop_set_indices(obj, y, z)

Arguments

obj	GatingHierarchy object
y	character node name or path
z	logical vector as local event indices relative to node y

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 <- gh_pop_get_stats(gh, nodes = c("CD3+", "CD4", "CD8"))
pop.stats

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

flowWorkspace documentation built on Nov. 8, 2020, 8:08 p.m.