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Plot distance density

Source: R/qc_visualizations.R
plot_dist_density.Rd

Plot density of distances between samples in QC samples and actual samples.

Usage

plot_dist_density(
  object,
  all_features = FALSE,
  dist_method = "euclidean",
  center = TRUE,
  scale = "uv",
  color_scale = getOption("notame.color_scale_dis"),
  fill_scale = getOption("notame.fill_scale_dis"),
  title = paste("Density plot of", dist_method, "distances between samples"),
  subtitle = NULL,
  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

method for calculating the distances, passed to dist

center

logical, should the data be centered?

scale

scaling used, as in prep Default is "uv" for unit variance

color_scale

a scale for the color of the edge of density curves, as returned by a ggplot function

fill_scale

a scale for the fill of the density curves, as returned by a ggplot function

title

the plot title

subtitle

the plot subtitle

assay.type

character, assay to be used in case of multiple assays

Value

A ggplot object.

See also

dist

Examples

data(example_set)
plot_dist_density(example_set)

# Drift correction tightens QCs together
plot_dist_density(correct_drift(example_set))
#> INFO [2025-06-23 22:37:39] 
#> Starting drift correction at 2025-06-23 22:37:39.926356
#> INFO [2025-06-23 22:37:39] Zero values in feature abundances detected. Zeroes will be replaced with 1.1.
#> INFO [2025-06-23 22:37:40] Drift correction performed at 2025-06-23 22:37:40.251752
#> INFO [2025-06-23 22:37:40] Inspecting drift correction results 2025-06-23 22:37:40.456545
#> INFO [2025-06-23 22:37:40] Drift correction results inspected at 2025-06-23 22:37:40.773323
#> INFO [2025-06-23 22:37:40] 
#> Drift correction results inspected, report:
#> Drift_corrected: 100%