plot_dendrogram: Draw dendrograms

In antonvsdata/notame: Workflow for non-targeted LC-MS metabolic profiling

Draw dendrograms

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 = getOption("notame.color_scale_dis")
)

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/notame documentation built on Sept. 14, 2024, 11:09 p.m.