plot.clustering: Consensus matrix heatmap

Description

Creates a heatmap of the (calibrated) consensus matrix. See examples in Clustering.

Usage

# S3 method for clustering
plot(
  x,
  linkage = "complete",
  argmax_id = NULL,
  theta = NULL,
  theta_star = NULL,
  col = c("ivory", "navajowhite", "tomato", "darkred"),
  lines = TRUE,
  col.lines = c("blue"),
  lwd.lines = 2,
  tick = TRUE,
  axes = TRUE,
  col.axis = NULL,
  cex.axis = 1,
  xlas = 2,
  ylas = 2,
  bty = "n",
  ...
)

Value

A heatmap.

Arguments

x: output of Clustering.
linkage: character string indicating the type of linkage used in hierarchical clustering to define the stable clusters. Possible values include "complete", "single" and "average" (see argument "method" in hclust for a full list).
argmax_id: optional indices of hyper-parameters. If argmax_id=NULL, the calibrated hyper-parameters are used.
theta: optional vector of cluster membership. If provided, the ordering of the items should be the same as in Clusters. This argument is used to re-order the consensus matrix.
theta_star: optional vector of true cluster membership. If provided, the ordering of the items should be the same as in Clusters. This argument is used to define item colours.
col: vector of colours.
lines: logical indicating if lines separating the clusters provided in theta should be displayed.
col.lines: colour of the lines separating the clusters.
lwd.lines: width of the lines separating the clusters.
tick: logical indicating if axis tickmarks should be displayed.
axes: logical indicating if item labels should be displayed.
col.axis: optional vector of cluster colours.
cex.axis: font size for axes.
xlas: orientation of labels on the x-axis, as las in par.
ylas: orientation of labels on the y-axis, as las in par.
bty: character string indicating if the box around the plot should be drawn. Possible values include: "o" (default, the box is drawn), or "n" (no box).
...: additional arguments passed to Heatmap.