ordination_plot: Ordination Plot

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description

This function allows for ordination (which helps us to distinguish beta diversity relationships) to be plotted as well as for the corresponding data to be returned.

Usage

ordination_plot(obj, method = "PCoA", distance = "wunifrac",
  color = "TreatmentGroup", title = NULL, only_data = FALSE)

Arguments

obj	An object to be converted to a taxmap object with create_taxmap.
method	Choose an ordination method from 'PCoA', 'CCA', 'NMDS' or 'DPCoA', Default: 'PCoA'
distance	Choose a distance method or use a pre-computed dist-class object, Default: 'wunifrac'
color	Choose the group or factor of which colors will be mapped to, Default: 'TreatmentGroup'
title	The title of the plot, Default: NULL
only_data	Allows for only ordination data to be generated, Default: FALSE

Value

By default, it returns an ordination plot.

See Also

View save_ordination_plots to save your ordination plot or multiple ordination plots.

Other Visualizations: alpha_diversity_plot, correlation_data, correlation_plots, correlation_plot, heat_tree_parameters, heat_tree_plots, ordination_plots, plot_limits, save_alpha_diversity_plots, save_correlation_plots, save_heat_tree_plots, save_ordination_plots, save_stacked_barplots, stacked_barplots, stacked_barplot, top_coefficients_barplot

Examples

## Not run: 
if (interactive()) {
  # An example ordination plot
  library(MicrobiomeR)
  data <- analyzed_silva
  plot <- ordination_plot(obj = data)
  plot
}

## End(Not run)

vallenderlab/MicrobiomeR documentation built on Aug. 30, 2019, 11:24 p.m.