ordination_plot: Multivariate analysis - Plot Ordination

In Coayala/MetaboTandem: Analysis and Visualization of LC-MS/MS Data

Multivariate analysis - Plot Ordination

Description

Function to plot ordination results

Usage

plot_ordination(
  ord_object,
  metadata,
  group_by,
  add_sample_names = FALSE,
  add_variables = FALSE,
  add_ellipse = FALSE,
  color_vector = NULL,
  abundances = NULL,
  plot = TRUE
)

plot_ordination.nmds(
  ord_object,
  metadata,
  group_by,
  add_sample_names,
  add_variables,
  add_ellipse,
  color_vector,
  abundances,
  plot
)

plot_ordination.pca(
  ord_object,
  metadata,
  group_by,
  add_sample_names,
  add_variables,
  add_ellipse,
  color_vector,
  plot
)

plot_ordination.pcoa(
  ord_object,
  metadata,
  group_by,
  add_sample_names,
  add_variables,
  add_ellipse,
  color_vector,
  abundances,
  plot
)

Arguments

ord_onj	Feature abundance table
method	Ordination method
distance	Dissimilarity distance to calculate. Available options are those from vegan::vegdist()

Value

Object returned depend on the selected method

Coayala/MetaboTandem documentation built on June 9, 2025, 9:02 p.m.