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Sample heatmap

Source: R/cluster_plots.R
plot_sample_heatmap.Rd

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 = NULL,
  title = "Heatmap of distances between samples",
  subtitle = NULL,
  fill_scale_con = getOption("notame.fill_scale_con"),
  fill_scale_dis = getOption("notame.fill_scale_dis"),
  assay.type = NULL
)

Arguments

object

a SummarizedExperiment or 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 as in dist

clust_method

method used in clustering as in hclust

center

logical, should the data be centered?

scale

scaling used, as in 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

assay.type

character, assay to be used in case of multiple assays

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

data(example_set)
plot_sample_heatmap(example_set, group = "Group")