heatmap.ddr: Flexible clustering function

In vdumeaux/mixtR: Matched Interaction across Tissues (MIxT) data analysis

Description

heatmap.ddr is a very flexible function for clustering. It allows multiple ways of specifying how the dendrogram is to be computed and it knows about the cor() and hclust() functions.

Usage

heatmap.ddr(exprs = NULL, dist.elem = "cor", clust.elem = "average",
  p = 2)

Arguments

exprs	a matrix-like object whose columns are to be clustered. May be omitted if a dendrogram can be obtained using only the other arguments.
dist.elem	specifies how to compute the distance matrix. May be omitted if a dendrogram can be obtained from 'clust.elem' alone. Possible specifications are: An object that can be coerced to a distance matrix (using as.dist()), a function that takes 'exprs' and produces a distance matrix, or a character string specifying how a distance matrix is to be computed from 'exprs'. The acceptable character strings are "cor" and any method specification that can be passed on to the dist() function. If 'dist.elem' is "cor", then 1-correlation (between the columns of 'exprs') is used as distance.
clust.elem	specifies how to compute the dendrogram. Possible specifications are: An object that can be coerced to "dendrogram" (using as.dendrogram()), a function that takes a distance matrix and produces an object that can be coerced to a dendrogram, a character string specifying how to compute, from a distance matrix, an object that can be coerced to a dendrogram, or a character string specifying how to compute a dendrogram from a distance matrix. passed to the dist() function and used only when 'dist.elem' is "minkowski" (see help on the dist() function for details).

vdumeaux/mixtR documentation built on May 3, 2019, 4:58 p.m.