R/query_multiple.R

In saeyslab/FlowSOM_workshop: How to get started with FlowSOM

#' query_multiple
#'
#' Function which takes a named list of multiple cell types, where every item is
#' a named vector with values "high"/"low" and the names correspond to the
#' markers or channels (e.g. as generated by parse_markertable).
#'
#' @param fsom FlowSOM object
#' @param ff FlowFrame used as reference for channel and marker names
#' @param cell_types Description of the cell types. Named list, with one named
#'                   vector per cell type containing "high"/"low" values
#' @param pdf_name Path to a pdf file to save figures
#'
#' @return A label for every FlowSOM cluster (Unknown or one of the celltype
#'         names of the list, if selected by QueryStarPlot)
#' @export
#'
#' @examples
#'
#'
query_multiple <- function(fsom,
                           ff,
                           cell_types,
                           pdf_name,
                           ...){

  if (class(fsom) == "list" & !is.null(fsom$FlowSOM)) {
    fsom <- fsom$FlowSOM
  }
  if (class(fsom) != "FlowSOM") {
    stop("fsom should be a FlowSOM object.")
  }

  labels <- rep("Unknown", fsom$map$nNodes)

  pdf(pdf_name,
      useDingbats = FALSE)
  for(cell_type in names(cell_types)){
    query <- cell_types[[cell_type]]
    names(query) <- get_channels(ff, names(query))
    query_res <- QueryStarPlot(fsom,
                               query = query,
                               main = cell_type,
                               equalNodeSize = TRUE)
    labels[query_res$selected] <- cell_type
  }
  dev.off()
  return(labels)
}