R/cluster_mat.R

In mssm-msf-2019/BiostatsALL:

#' function for pheatmap
#' @description function for pheatmap
#' @export

cluster_mat = function(mat, distance, method){
  if(!(method %in% c("ward.D", "ward.D2", "ward", "single", "complete", "average", "mcquitty", "median", "centroid"))){
    stop("clustering method has to one form the list: 'ward', 'ward.D', 'ward.D2', 'single', 'complete', 'average', 'mcquitty', 'median' or 'centroid'.")
  }
  if(!(distance[1] %in% c("correlation", "euclidean", "maximum", "manhattan", "canberra", "binary", "minkowski")) & class(distance) != "dist"){
    stop("distance has to be a dissimilarity structure as produced by dist or one measure  form the list: 'correlation', 'euclidean', 'maximum', 'manhattan', 'canberra', 'binary', 'minkowski'")
  }
  if(distance[1] == "correlation"){
    d = as.dist(1 - cor(t(mat)))
  }
  else{
    if(class(distance) == "dist"){
      d = distance
    }
    else{
      d = dist(mat, method = distance)
    }
  }

  return(hclust(d, method = method))
}