plot_dist_density: Distance density plot

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

Distance density plot

Description

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
)

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	method for calculating the distances, passed to dist
center	logical, should the data be centered?
scale	scaling used, as in pcaMethods::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

Value

a ggplot object

See Also

dist

Examples

plot_dist_density(merged_sample)
# Drift correction tightens QCs together
plot_dist_density(correct_drift(merged_sample))

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