R/fcTree-methods.R

In openCyto: Hierarchical Gating Pipeline for flow cytometry data

#' get nodes from \code{fcTree}
#'
#' @param x \code{fcTree}
#' @param y \code{character} node name
#' @aliases getNodes,fcTree-method
setMethod("getNodes", signature = c("fcTree"), definition = function(x, y) {
  if (missing(y)) {
    nodeData(x)
  } else {
    nodeData(x, y)
  }
})
#' get gates saved in \code{fcTree}
#'
#' @param obj \code{fcTree}
#' @param y \code{character} node name
#' @param ... other arguments (not used)
#' @aliases getGate,fcTree,character-method
setMethod("getGate", sig = c("fcTree", "character"),
    definition = function(obj, y,  ...) {
      # get filterList
      matchedNode <-.getNode(obj,y,...)
      flist <- matchedNode[["fList"]]
      flist
    })

.getNode<-function(x,y,..){
  nodes <- getNodes(x)
  
  allAlias <- lapply(nodes, function(curNode) alias(curNode$pop))
  ind <- which(allAlias %in% y)
  if (length(ind) > 1) {
    stop("Population '", y, "' is ambiguous!")
  } else if (length(ind) == 0) {
    stop("Population '", y, "' is not found!")
  } else {
    matchedNode <- nodes[[ind]]
  }
  matchedNode
}

#' plot the flowClust gating results
#' 
#' This provides the priors and posteriors as well as the gates for the purpose of debugging flowClust gating algorithm
#' 
#' @param x \code{fcTree}
#' @param y \code{character} node name in the \code{fcTree}
#' @param channel \code{character} specifying the channel.
#' @param data \code{GatingSet} that the \code{fcTree} is associated with
#' @param ... other arguments
setMethod("plot", sig = c("fcTree", "character"),
          definition = function(x, y, channel = NULL, data = NULL,...) {
  # get filterList
#      browser()
    flist <- getGate(x,y)
    matchedNode <-.getNode(x,y)
    if(!is.null(data))
      parentNode <- gs_pop_get_parent(data[[1]],y)
  plot(x = flist, y = channel, main = matchedNode$pop@name, node =parentNode, data = data, ...)
})

#setMethod("plot", sig = c("fcTree", "numeric"),
#          definition = function(x, y, channel = NULL, ...) {
#  y <- as.character(y)
#  nodes <- getNodes(x)
#  matchedNode <- nodes[[y]]
#  fcObj <- matchedNode$fcObj
#  
#  plot(x = fcObj, y = channel, main = matchedNode$pop@name, ...)
#})