Ordination Plot

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.

Generate plots for a list of ordination methods and distances.

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

ordination_plots(
  obj,
  methods = c("PCoA", "NMDS"),
  distances = c("wunifrac", "unifrac", "bray"),
  color = "TreatmentGroup",
  select_otu_table = "otu_proportions"
)

Arguments

obj

An object to be converted to a metacoder 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

methods

A list of ordination methods, Default: 'c("PCoA", "NMDS")'

distances

A list of distance methods, Default: 'c("wunifrac", "unifrac", "bray")'

select_otu_table

The data table to use in the observation data. Default: "otu_proportions"

Value

By default, it returns an ordination plot.

Returns a melted dataframe.

See also

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

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

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

Examples

if (FALSE) { # \dontrun{
if (interactive()) {
  # An example ordination plot
  library(MicrobiomeR)
  data <- analyzed_silva
  plot <- ordination_plot(obj = data)
  plot
}
} # }