R/fortify_fs.R

In ggcyto: Visualize Cytometry data with ggplot

#' Fortify a model into flowSet object
#'
#' The method provides a universe interface to convert a generic R object into a flowSet useful for ggcyto
#'
#' @param model flow object(flowFrame or GatingSet) to be converted to flowSet. when it is a GatingSet, it must contain the subset information stored as  'subset' attribute.
#' @param data original dataset, if needed
#' @param ... other arguments passed to methods
#' @return a flowSet/ncdfFlowSet object
#' @examples 
#' data(GvHD)
#' fr <- GvHD[[1]]
#' fortify_fs(fr)
#' 
#' dataDir <- system.file("extdata",package="flowWorkspaceData")
#' gs <- load_gs(list.files(dataDir, pattern = "gs_manual",full = TRUE))
#' attr(gs, "subset") <- "CD4"
#' fortify_fs(gs)
#' @export
fortify_fs <- function(model, data, ...) UseMethod("fortify_fs")

#' @rdname fortify_fs
#' @export
fortify_fs.flowSet <- function(model, data, ...) model

#' @rdname fortify_fs
#' @export
fortify_fs.default <- function(model, data, ...) {
  
  stop("ggcyto doesn't know how to deal with data of class ", class(model), call. = FALSE)
}




#' @export
#' @rdname fortify_fs
fortify_fs.flowFrame <- function(model, data, ...){
  sn <- identifier(model)
  fs <- as(model, "flowSet")
  if(nchar(sn) > 0){
    sampleNames(fs) <- sn
    pData(fs)[["name"]] <- sn
  }
    
  fs
}

#' @export
#' @rdname fortify_fs
fortify_fs.GatingSetList <- function(model, data, ...){
  getS3method("fortify_fs", "GatingSet")(model, data, ...)
}
#' @export
#' @rdname fortify_fs
fortify_fs.GatingSet <- function(model, data, ...){
  
  subset <- attr(model, "subset")
  if(is.null(subset))
    stop("subset must be supplied!")
  else if(subset == "_parent_")
    stop("'subset' must be instantiated by the actual node name!\nMake sure either 'subset' is specified or the 'geom_gate' layer is added. ")
  fs <- gs_pop_get_data(model, subset)  
  
  
  #copy dims attribute to fs
  attr(fs, "dims") <- attr(model, "dims")
  attr(fs, "filter") <- attr(model, "filter")
  fs
  
}