Removed Marc's custom factoextra functions

modules/auxfunc.R

@@ -597,106 +597,6 @@ getClCol <- function(in.dend, in.k) {
   ))
 }
 
-# Cluster validation ----
-
-#Customize factoextra functions to accept dissimilarity matrix from start. Otherwise can't use distance functions that are not in base R, like DTW.
-
-# Inherit and adapt hcut function to take input from UI, used for fviz_clust
-LOChcut <-
-  function(x,
-           k = 2,
-           isdiss = inherits(x, "dist"),
-           hc_func = "hclust",
-           hc_method = "average",
-           hc_metric = "euclidean") {
-    if (!inherits(x, "dist")) {
-      stop("x must be a distance matrix")
-    }
-    return(
-      factoextra::hcut(
-        x = x,
-        k = k,
-        isdiss = TRUE,
-        hc_func = hc_func,
-        hc_method = hc_method,
-        hc_metric = hc_metric
-      )
-    )
-  }
-
-# Modified from factoextra::fviz_nbclust
-# Allow (actually enforce) x to be a distance matrix; no GAP statistics for compatibility
-LOCnbclust <-
-  function (x,
-            FUNcluster = LOChcut,
-            method = c("silhouette", "wss"),
-            k.max = 10,
-            verbose = FALSE,
-            barfill = "steelblue",
-            barcolor = "steelblue",
-            linecolor = "steelblue",
-            print.summary = TRUE,
-            ...)
-  {
-    set.seed(123)
-    
-    if (k.max < 2)
-      stop("k.max must bet > = 2")
-    
-    method = match.arg(method)
-    
-    if (!inherits(x, c("dist")))
-      stop("x should be an object of class dist")
-    else if (is.null(FUNcluster))
-      stop(
-        "The argument FUNcluster is required. ",
-        "Possible values are kmeans, pam, hcut, clara, ..."
-      )
-    else if (method %in% c("silhouette", "wss")) {
-      diss <- x  # x IS ENFORCED TO BE A DISSIMILARITY MATRIX
-      v <- rep(0, k.max)
-      if (method == "silhouette") {
-        loc.mainlab = "Optimal number of clusters from silhouette analysis"
-        loc.ylab <- "Average silhouette width"
-        
-        for (i in 2:k.max) {
-          clust <- FUNcluster(x, i, ...)
-          v[i] <-
-            factoextra:::.get_ave_sil_width(diss, clust$cluster)
-        }
-      }
-      else if (method == "wss") {
-        loc.mainlab = "Optimal number of clusters from within cluster sum of squares"
-        loc.ylab <- "Total within cluster sum of squares"
-        
-        for (i in 1:k.max) {
-          clust <- FUNcluster(x, i, ...)
-          v[i] <- factoextra:::.get_withinSS(diss, clust$cluster)
-        }
-      }
-      
-      df <- data.frame(clusters = as.factor(1:k.max), y = v)
-      
-      p <- ggpubr::ggline(
-        df,
-        x = "clusters",
-        y = "y",
-        group = 1,
-        color = linecolor,
-        ylab = loc.ylab,
-        xlab = "Number of clusters",
-        main = loc.mainlab
-      )
-      
-      if (method == "silhouette")
-        p <- p + geom_vline(xintercept = which.max(v),
-                            linetype = 2,
-                            color = linecolor)
-      return(p)
-    }
-  }
-
-
 # Custom plotting functions ----