Plotting core microbiota on ordinations

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

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")

Value

plot

Details

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

Examples

if (FALSE) {

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
}