R/gating_subset.R

In saeyslab/FlowSOM_workshop: How to get started with FlowSOM

#' Select only a subset of cells
#'
#' Given a parsed flowjo result,
#' return only those cells which fall into a specific gate
#'
#' @param flowjo_res The parsed flowjo result, as generated by parse_flowjo
#' @param gate       The name of the gate that should be used for selection
#'
#' @return Returns a list with two elements: flowFrame/flowSet and gates. Both are
#' subsetted to contain only the cells of interest.
#'
#' @export
gating_subset <- function(flowjo_res, gate){

  if(!is.null(flowjo_res$flowSet)){
    res <- lapply(seq_len(length(flowjo_res$flowSet)),
                  function(i){
                    flowjo_res$flowSet[[i]][flowjo_res$gates[[i]][,gate],]
                  })
    names(res) <- sampleNames(flowjo_res$flowSet)
    return(list(
      flowSet = flowCore::flowSet(res),
      gates = lapply(flowjo_res$gates, function(x)x[x[,gate], ])
    ))

  } else {
    return(list(flowFrame = flowjo_res$flowFrame[flowjo_res$gates[,gate], ],
                gates = flowjo_res$gates[flowjo_res$gates[,gate], ]))
  }
}