R/data_add_graphs.R

In IFC: Tools for Imaging Flow Cytometry

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# This file is released under the GNU General Public License, Version 3, GPL-3 #
# Copyright (C) 2022 Yohann Demont                                             #
#                                                                              #
# It is part of IFC package, please cite:                                      #
# -IFC: An R Package for Imaging Flow Cytometry                                #
# -YEAR: 2020                                                                  #
# -COPYRIGHT HOLDERS: Yohann Demont, Gautier Stoll, Guido Kroemer,             #
#                     Jean-Pierre Marolleau, Loïc Garçon,                      #
#                     INSERM, UPD, CHU Amiens                                  #
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#' @title Add Graphs to IFC_data Object
#' @description
#' Adds graphs to an already existing `IFC_data` object.
#' @param obj an `IFC_data` object extracted by ExtractFromDAF(extract_features = TRUE) or ExtractFromXIF(extract_features = TRUE).
#' @param graphs a list of graph(s) to add to obj. Each element of this list will be coerced by \code{\link{buildGraph}}.
#' @param adjust_graph whether to try to adjust graph(s) when possible. Default is TRUE.\cr
#' -TRUE, graph(s) will be kept if possible using only regions, pops it depends that can be found in 'obj',\cr
#' -FALSE, graph(s) will be kept only if all features, regions, pops it refers to are found in 'obj',\cr
#' -NA, is not allowed and will throw an error.
#' @param ... Other arguments to be passed.
#' @return an IFC_data object with graphs added.
#' @export
data_add_graphs <- function(obj, graphs, adjust_graph=TRUE, ...) {
  assert(obj, cla = "IFC_data")
  adjust_graph = as.logical(adjust_graph)
  assert(adjust_graph, len = 1, alw = c(TRUE,FALSE))
  L = length(obj$graphs)
  if(L == 0) obj$graphs = list()
  for(i in seq_along(graphs)) {
    g = adjustGraph(obj = obj, graph = graphs[[i]], adjust_graph = adjust_graph)
    if(length(g) == 0) {
      stop("can't add element [",i,"] of 'graphs' to 'obj'") 
    } else {
      obj$graphs = c(obj$graphs, list(g))
    }
  }
  class(obj$graphs) <- "IFC_graphs"
  return(obj)
}