R/nodeSize.R

In JulianSpagnuolo/FACkit: FACS Analysis Tool Kit

nodeSize <- function(somtree, reset=FALSE, maxNodeSize=0.1)
{
  #' @title Scaled Node Sizes for growing SOM
  #' @author Julian Spagnuolo
  #' @description calcs size of nodes for som tree
  #' @param somtree results from calling som.tree
  #' @param reset Logical. If TRUE, node size is reset to maxNodeSize, default = FALSE
  #' @param maxNodeSize Maximum size for any node. Default = 15
  #'
  #'
  #'
  #'
  #'
  #'
  #'
  #'
  if(somtree$algorithm == "GrowSOM")
  {
    if(reset == TRUE)
    {
      somtree$map$nodes$size <- as.vector(rep(maxNodeSize, nrow(somtree$map$nodes$codes)))
    }
    else
    {
      t <- table(somtree$map$mapped$bmn)
      t <- sqrt(t)
      scale <- max(t)
      rescaled <- maxNodeSize * t/scale
      somtree$map$nodes$size <- numeric(nrow(somtree$map$nodes$codes))
      somtree$map$nodes$size[as.numeric(names(t))] <- as.vector(rescaled)
    }
  }

  if(somtree$algorithm == "kohonen")
  {
    somtree$map$nodes <- list()
    if(reset == TRUE)
    {
      somtree$map$nodes$size <- as.vector(rep(maxNodeSize, nrow(somtree$som$codes[[1]])))
    }
    else
    {
      t <- table(somtree$map$unit.classif)
      t <- sqrt(t)
      scale <- max(t)
      rescaled <- maxNodeSize * t/scale
      somtree$map$nodes$size <- numeric(nrow(somtree$som$codes[[1]]))
      somtree$map$nodes$size[as.numeric(names(t))] <- as.vector(rescaled)
    }
  }

  if(somtree$algorithm == "dm")
  {
    somtree$map$nodes <- list()
    if(reset == TRUE)
    {
      somtree$map$nodes$size <- as.vector(rep(maxNodeSize, nrow(somtree$som$codes[[1]])))
    }
    else
    {
      t <- table(somtree$map$unit.classif)
      t <- sqrt(t)
      scale <- max(t)
      rescaled <- maxNodeSize * t/scale
      somtree$map$nodes$size <- numeric(nrow(somtree$som$codes[[1]]))
      somtree$map$nodes$size[as.numeric(names(t))] <- as.vector(rescaled)
    }
  }

  somtree
}