plot.clustering {sharp}

Consensus matrix heatmap

Description

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

Usage

## S3 method for class '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",
  ...
)

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.

Value

A heatmap.