plot_dendrogram: Draw dendrograms

In antonvsdata/amp: Smoothing Metabolomics Analyses

Description

Draws a dendrogram of a hierarchical clustering applied to the samples of an experiment

Usage

plot_dendrogram(object, all_features = FALSE,
  color = group_col(object), dist_method = "euclidean",
  clust_method = "ward.D2", center = TRUE, scale = "uv",
  title = "Dendrogram of hierarchical clustering", subtitle = NULL,
  color_scale = NULL)

Arguments

object	a MetaboSet object
all_features	logical, should all features be used? If FALSE (the default), flagged features are removed before visualization.
color	character, name of the column used for coloring the sample labels
dist_method	distance method used in clustering, see ?dist
clust_method	method used in clustering, see ?hclust
center	logical, should the data be centered?
scale	scaling used, as in pcaMethods::prep. Default is "uv" for unit variance
title	The plot title
subtitle	The plot subtitle
color_scale	the color scale as returned by a ggplot function

Value

A ggplot object.

See Also

dist hclust

Examples

plot_dendrogram(merged_sample)

antonvsdata/amp documentation built on Jan. 8, 2020, 3:15 a.m.