R/layer_info.R

In granar/granar: Generator of Root ANAtomy in R

#' @title Get the coordinate of the first cell center
#'
#'
#' @param all_layers The layer dataframe
#' @keywords root layer
#' @export
#'

layer_info <- function(all_layers){

  all_layers$radius <- all_layers$cell_diameter / 2
  all_layers$perim <- all_layers$radius * 2 * pi
  all_layers$n_cell <- 1
  all_layers$angle_inc <- 0

  all_layers$radius[1] <- 0
  multi <- 1

  for(i in c(2:nrow(all_layers))){
    # Update radius
    all_layers$radius[i] <- all_layers$radius[i-1] + all_layers$cell_diameter[i-1] / 2 + all_layers$cell_diameter[i] / 2

    if(all_layers$name[i] == "pericyle" & multi == 1){
      all_layers$radius[i] <- stele_diameter/2 + all_layers$cell_diameter[i] / 2
      multi <- 2 # in case there is more than one pericycle layer
    }
    # Update perimeter
    all_layers$perim[i] <- all_layers$radius[i] * 2 * pi

    # Update number of cells in the layers
    all_layers$n_cell[i] <- round(all_layers$perim[i] / all_layers$cell_diameter[i])

    # Update the mean angle between cells
    all_layers$angle_inc[i] <- 2 * pi / all_layers$n_cell[i]
  }

  return(all_layers)
}