plot_ordination_utils: Plot species loading with ordinations

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Plot species loading with ordinations

Description

This function extends the plot_ordination function of phyloseqto highlight the top taxa loadings on the species ordination.

Usage

plot_ordination_utils(
  x,
  ordiObject,
  color.opt = NULL,
  plot.arrow = TRUE,
  scale.arrow = NULL,
  top.taxa = 5
)

Arguments

x	phyloseq-class object
ordiObject	Output of ordinate from package phyloseq. Only NMDS/CCA and Bray supported.
color.opt	Variable of interest from metadata.
plot.arrow	If arrow should be plotted for species either TRUE or FALSE.
scale.arrow	If arrow is plotted a constant to multiply axis values for clearing visualisations.
top.taxa	Top varying taxa to plot, default is 5.

Details

This function is useful for visualizing specifc taxa that could be important in explaining variations in ordinations.

Value

plot

Examples

## Not run: 

library(microbiomeutilities)
library(RColorBrewer)
data("zackular2014")
ps1 <- zackular2014
ps2 <- tax_glom(ps1, "Genus")
ps2f <- format_to_besthit(ps2)
orddi <- ordinate(ps2f, method = "CCA", distance = "bray")
p <- plot_ordination_utils(ps2f, orddi,
  color = "DiseaseState", plot.arrow = TRUE,
  scale.arrow = 1.3, top.taxa = 5
)
print(p)

## End(Not run)

microsud/microbiomeutilities documentation built on Nov. 29, 2022, 12:18 a.m.