plot_ordination: Generate an Ordination Plot

In leffj/mctoolsr: Microbial Community Data Analysis Tools

Generate an Ordination Plot

Description

Used to generate a plot from the output of calc_ordination()

Usage

plot_ordination(
  input,
  ordination_axes,
  color_cat,
  shape_cat,
  hulls = FALSE,
  ...
)

Arguments

input	The input dataset as loaded by load_taxa_table().
ordination_axes	The output of calc_ordination().
color_cat	The metadata map header used to color points.
shape_cat	The metadata map header used for points' shapes (optional).
hulls	Whether or not to include an outline around sample categories.
...	Additional arguments passed to ggplot2's geom_point().

Examples

fvrar = single_rarefy(fruits_veggies, 100)
ord = calc_ordination(calc_dm(fvrar$data_loaded), 'nmds')
plot_ordination(fvrar, ord, 'Sample_type', 'Farm_type', hulls = TRUE)

leffj/mctoolsr documentation built on Aug. 5, 2022, 1:27 a.m.