R/create_cells.R

In granar/granar: Generator of Root ANAtomy in R

#' @title Create cells space
#'
#' Place initial position of the cell center
#' @param all_layers The layer dataframe
#' @param random_fact The random factor
#' @keywords root
#' @export
#' @examples
#' # all_cells = create_cells(all_layers, random_fact)
#'

create_cells <- function(all_layers, random_fact){

  center <- max(all_layers$radius)
  all_cells <- NULL
  k <- 1
  for(i in c(1:nrow(all_layers))){
    radius <- all_layers$radius[i]
    if(all_layers$angle_inc[i] > 0){
      angles <- seq(from = 0, to = (2*pi), by = all_layers$angle_inc[i])[-1]
    }else{
      angles <- 0
    }
    k1 <- k+all_layers$n_cell[i]-1
    ks <- c(k:k1)
    k <- k1+1

    if(all_layers$name[i] == "outside"){
      x <- center + (radius * cos(angles))
      y <- center + (radius * sin(angles))
    }else if(all_layers$name[i] == "stele"){
      x <- center + (radius * cos(angles)) + stats::runif(all_layers$n_cell[i], -random_fact, random_fact)#* runif(all_layers$n_cell[i], 1-(random_fact*2), 1+(random_fact*2))
      y <- center + (radius * sin(angles)) + stats::runif(all_layers$n_cell[i], -random_fact, random_fact)
    }else if(substr(all_layers$name[i], 1,6) == "cortex"){
      x <- center + (radius * cos(angles)) + stats::runif(all_layers$n_cell[i], -random_fact*3, random_fact*3)#* runif(all_layers$n_cell[i], 1-(random_fact*2), 1+(random_fact*2))
      y <- center + (radius * sin(angles)) + stats::runif(all_layers$n_cell[i], -random_fact*3, random_fact*3)##* runif(all_layers$n_cell[i], 1-(random_fact*2), 1+(random_fact*2))
    }else{
      x <- center + (radius * cos(angles)) + stats::runif(all_layers$n_cell[i], -random_fact, random_fact)#* runif(all_layers$n_cell[i], 1-random_fact, 1+random_fact)
      y <- center + (radius * sin(angles)) + stats::runif(all_layers$n_cell[i], -random_fact, random_fact)#* runif(all_layers$n_cell[i], 1-random_fact, 1+random_fact)
    }

    all_cells <- rbind(all_cells, data.frame(
      angle = angles,
      radius = radius,
      x = x,
      y = y,
      id_layer = i,
      id_cell = ks,
      type = all_layers$name[i],
      order = all_layers$order[i]
    )
    )
  }

  return(all_cells)
}