ordination_plots: Ordination Plots

In vallenderlab/MicrobiomeR: Analyze Microbiome Data

Description

Generate plots for a list of ordination methods and distances.

Usage

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.
methods	A list of ordination methods, Default: 'c("PCoA", "NMDS")'
distances	A list of distance methods, Default: 'c("wunifrac", "unifrac", "bray")'
color	Choose the group or factor of which colors will be mapped to, Default: 'TreatmentGroup'
select_otu_table	The data table to use in the observation data. Default: "otu_proportions"

Value

Returns a melted dataframe.

See Also

Other Visualizations: alpha_diversity_plot, correlation_data, correlation_plots, correlation_plot, heat_tree_parameters, heat_tree_plots, ordination_plot, 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

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