Diff of /R/getSilhouette.R [000000] .. [494cbf]

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+#' @name getSilhouette
+#' @title Get silhoutte plot from consensus clustering
+#' @description This function visualizes the silhoutte information.
+#' @param sil A sil object returned from `getConsensusMOIC()`.
+#' @param clust.col A string vector storing colors for annotating each cluster.
+#' @param fig.path A string value to indicate the output path for storing the consensus heatmap.
+#' @param fig.name A string value to indicate the name of the consensus heatmap.
+#' @param width A numeric value to indicate the width of output figure.
+#' @param height A numeric value to indicate the height of output figure.
+#' @return A silhoutte barplot.
+#' @export
+#' @import cluster
+#' @importFrom grDevices dev.copy2pdf
+#' @examples # There is no example and please refer to vignette.
+getSilhouette <- function(sil       = NULL,
+                          clust.col = c("#2EC4B6", "#E71D36", "#FF9F1C", "#BDD5EA", "#FFA5AB", "#011627","#023E8A","#9D4EDD"),
+                          fig.path  = getwd(),
+                          fig.name  = "silhoutte",
+                          width     = 5.5,
+                          height    = 5) {
+
+  N.clust <- length(unique(sil[,1]))
+  colvec <- clust.col[1:N.clust]
+
+  outFig <- paste0(fig.name,".pdf")
+  par(bty="o", mgp = c(2.5,0.33,0), mar=c(5.1,2.1,3.1,2.1)+.1, las=1, tcl=-.25)
+  plot(sil,
+       border = NA,
+       col = colvec)
+  dev.copy2pdf(file = file.path(fig.path, outFig), width = width, height = height)
+}