R/bacteriaFlowFrame.R

In ucl-cssb/autoGate: Tool for Removing Background Debris and Doublets From .fcs Files

get.bacteria <- function(flow_frame, pre_cleaned) {
  if(pre_cleaned){
    best.clusters <- flowClust::flowClust(flow_frame,
                                         varNames = c("FSC-H", "SSC-H"),
                                         K = 1,
                                         level = 0.90);

    bact_flow_frame <- flow_frame[best.clusters,]

    return(bact_flow_frame)
  } else {

    ## calculate clusters for K=1 and K=2
    all_clusters <- flowClust::flowClust(flow_frame,
                                         varNames = c("FSC-H", "SSC-H"),
                                         K = 1:2,
                                         criterion = "ICL",
                                         level = 0.90);

    ## get the results for the K with the best ICL
    best.clusters <- all_clusters[[all_clusters@index]]
    print(paste(best.clusters@K, "clusters found"))

    if (best.clusters@K == 2) { ## if there are two cluster
      bact.indx <- which(flowClust::getEstimates(all_clusters[[2]], flow_frame)$locationsC[,2]
                         == max(flowClust::getEstimates(all_clusters[[2]], flow_frame)$locationsC[,2]))

      clst.fsc <- flowClust::getEstimates(all_clusters[[2]], flow_frame)$locationsC[[bact.indx, 1]]
      clst.ssc <- flowClust::getEstimates(all_clusters[[2]], flow_frame)$locationsC[[bact.indx, 2]]

      if ((clst.fsc < 4) && (clst.ssc < 3)) {
        print("only debris found")
        bact_flow_frame <- 0
      } else {
        Ks <- seq(1:2)
        debris.clusts <- setdiff(Ks, bact.indx)
        split_flow_frame <- flowClust::split(flow_frame, best.clusters,
                                             population = list(debris = debris.clusts,
                                                               non.debris = bact.indx))
        bact_flow_frame <- split_flow_frame$non.debris
      }

    }
    else { ## if there is only one cluster
      clst.fsc <- flowClust::getEstimates(best.clusters, flow_frame)$locationsC[[1]]
      clst.ssc <- flowClust::getEstimates(best.clusters, flow_frame)$locationsC[[2]]
      if ((clst.fsc < 4) && (clst.ssc < 3)) {
        print("only debris found")
        bact_flow_frame <- 0
      } else {
        bact_flow_frame <- flow_frame[best.clusters,]
      }
    }

    return(bact_flow_frame)
  }
}