plot_ordiplot_core: Plotting core microbiota on ordinations

In microsud/microbiomeutilities: microbiomeutilities: Utilities for Microbiome Analytics

Plotting core microbiota on ordinations

Description

This function will plot the ordaination along with highligthing the core microbes on the species ordination.

Usage

plot_ordiplot_core(
  x,
  ordiObject,
  prevalences,
  detections,
  min.prevalence,
  color.opt,
  shape,
  Samples = c(TRUE, FALSE)
)

Arguments

x	phyloseq-class object
ordiObject	Output of ordinate from package phyloseq. Only NMDS and Bray supported.
prevalences	Prevalences as supported by microbiome package.
detections	Detections as supported by microbiome package.
min.prevalence	Minimum prevalence value to plot.
color.opt	Variable of interest from metadata.
shape	Variable of interest from metadata.
Samples	c("TRUE" or "FALSE")

Details

This function is useful for visualizing core taxa in a 2D ordination plot.

Value

plot

Examples

## Not run: 

library(microbiomeutilities)
library(RColorBrewer)
data("zackular2014")
p0 <- zackular2014
ps1 <- format_to_besthit(p0)
ps1 <- subset_samples(ps1, DiseaseState == "H")
ps1 <- prune_taxa(taxa_sums(ps1) > 0, ps1)
prev.thres <- seq(.05, 1, .05)
det.thres <- 10^seq(log10(1e-4), log10(.2), length = 10)
pseq.rel <- microbiome::transform(ps1, "compositional")
ord.bray <- ordinate(pseq.rel, "NMDS", "bray")

p <- plot_ordiplot_core(pseq.rel, ord.bray,
  prev.thres, det.thres,
  min.prevalence = 0.9,
  color.opt = "DiseaseState", shape = NULL, Sample = TRUE
)
p

## End(Not run)

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