GetThresholdedIntensities: Extract Thresholded Intensities from a GatingSet
In COMPASS: Combinatorial Polyfunctionality Analysis of Single Cells

Description Usage Arguments Details Value Examples

View source: R/GetThresholdedIntensities.R

This function extracts thresholded intensities for children of a node node, as specified through the map argument.

1	GetThresholdedIntensities(gs, node, map)

`gs`	A `GatingSet` or `GatingSetList`.
`node`	The name, or path, of a single node in a `GatingSet` / `GatingSetList`.
`map`	A `list`, mapping node names to markers.

map should be an R list, mapping node names (as specified in the gating hierarchy of the gating set) to channel names (as specified in either the desc or name columns of the parameters of the associated flowFrames in the GatingSet).

A list with two components:

`data`	A `list` of thresholded intensity measures.
`counts`	A named vector of total cell counts at the node `node`.

if (require("flowWorkspace")&require("flowCore")&require("tidyr")) {

  ## Generate an example GatingSet that could be used with COMPASS
  ## We then pull out the 'data' and 'counts' components that could
  ## be used within a COMPASSContainer

  n <- 10 ## number of samples
  k <- 4 ## number of markers

  sid_vec <- paste0("sid_", 1:n) ## sample ids; unique names used to denote samples
  iid_vec <- rep_len( paste0("iid_", 1:(n/10) ), n ) ## individual ids
  marker_names <- c("TNFa", "IL2", "IL4", "IL6")

  ## Generate n sets of 'flow' data -- a list of matrices, each row
  ## is a cell, each column is fluorescence intensities on a particular
  ## channel / marker
  data <- replicate(n, {
    nrow <- round(runif(1) * 1E4 + 1000)
    ncol <- k
    vals <- rexp( nrow * ncol, runif(1, 1E-5, 1E-3) )
    output <- matrix(vals, nrow, ncol)
    colnames(output) <- marker_names
    return(output)
  })
  names(data) <- sid_vec

  ## Put it into a GatingSet
  fs <- flowSet( lapply(data, flowFrame) )
  gs <- GatingSet(fs)

  ## Add some dummy metadata
  meta <- pData(gs)
  meta$PTID <- 1:10
  pData(gs) <- meta

  gate <- rectangleGate( list(TNFa=c(-Inf,Inf)))
  gs_pop_add(gs, gate, parent="root", name="dummy")

  ## Add dummy gate

  ## Make some gates, and apply them
  invisible(lapply(marker_names, function(marker) {
    .gate <- setNames( list( c( rexp(1, runif(1, 1E-5, 1E-3)), Inf) ), marker )
    gate <- rectangleGate(.gate=.gate)
    gs_pop_add(gs, gate, parent="dummy", name=paste0(marker, "+"))
  }))

  recompute(gs)

  ## Map node names to channel names
  map=list(
    "TNFa+"="TNFa",
    "IL2+"="IL2",
    "IL4+"="IL4",
    "IL6+"="IL6"
  )

  ## Pull out the data as a COMPASS-friendly dataset
  node <- "dummy"
  map <- map
  system.time(
    output <- GetThresholdedIntensities(gs, "dummy", map)
  )

  system.time(
    output <- COMPASSContainerFromGatingSet(gs, "dummy", individual_id="PTID")
  )

  str(output)

}