plot_sample_heatmap: Draw heatmaps

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

Draw heatmaps

Description

Draws a heatmap of the distances between the samples of an experiment, the samples are ordered by hierarchical clustering.

Usage

plot_sample_heatmap(
  object,
  all_features = FALSE,
  dist_method = "euclidean",
  clust_method = "ward.D2",
  center = TRUE,
  scale = "uv",
  group_bar = TRUE,
  group = group_col(object),
  title = "Heatmap of distances between samples",
  subtitle = NULL,
  fill_scale_con = getOption("notame.fill_scale_con"),
  fill_scale_dis = getOption("notame.fill_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.
dist_method	distance method used in clustering, see dist
clust_method	clustering 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
group_bar	logical, should a bar showing the groups be drawn under the heat map?
group	character, name of the column used for coloring the group bar
title	The plot title
subtitle	The plot subtitle
fill_scale_con	Continuous fill scale for the heatmap as returned by a ggplot function
fill_scale_dis	Discrete fill scale for the group bar as returned by a ggplot function

Value

a ggplot object. If group_bar is TRUE, the plot will consist of multiple parts and is harder to modify.

See Also

dist hclust

Examples

plot_sample_heatmap(merged_sample)

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