plotPCoA: PCoA plot

In RIVM-IIV-Microbiome/biomeViz: Data visualization for microbiome analytics

PCoA plot

Description

PCoA plot

Arguments

x	phyloseq-class object.
group_var	A column in sample_data to compare. This is also the variable used to colour.
ord_method	Ordination method, currently tested PCoA.
dist_method	Distance method, currently tested Bray-Curtis.
seed	Random seed number set.seed.
cor_method	Correlation method. Default is Spearman.
padj_cutoff	Cut-off for multiple testing. Default is 0.05.
padj_method	Method for multiple testing. Default is fdr.
arrows	Logical. If arrows for taxa with correlation to axis are to be plotted. Default is TRUE.
label_col	Color of labels. Default is grey30.
plot_centroids	Logical. To plot centroids or not. Default is TRUE.
add_side_box	Logical. To plot side boxplots or not. Default is TRUE.
axis_plot	Which axis to plot. Default is first two.
point_shape	Shape of the points. Default is 21.
point_alpha	Opacity of points. Default is 0.5
verbose	Logical. Messages to print. Default is TRUE.
...	Additional arguments to pass to vegan's adonis function.

Details

A Principal Coordinates Analysis for phyloseq-class object. To visualize similarities or dissimilarities between samples in 2D ordination. This function extends the phyloseq ordination plots to include taxa that correlate with choosen axis and plots them along with a side boxplot for comparing inter-sample variation within groups.

Value

a ggplot2 object.

Author(s)

Sudarshan A. Shetty

References

Shetty SA (2021). Data visualization for microbiome analytics. https://github.com/microsud/biomeViz

Examples

library(biomeUtils)
library(dplyr)
library(ggside)
ps <- FuentesIliGutData %>%
  microbiome::transform("compositional") %>%
  mutateTaxaTable(FeatureID = taxa_names(FuentesIliGutData))
plotPCoA(x =ps,
         group_var = "ILI",
         ord_method = "PCoA",
         dist_method = "bray",
         seed = 1253,
         cor_method = "spearman",
         verbose = TRUE,
         padj_cutoff = 0.05,
         padj_method = "fdr",
         arrows = TRUE,
         label_col = "grey30",
         plot_centroids = TRUE,
         add_side_box = TRUE,
         axis_plot = c(1:2),
         point_shape = 21,  # point_shape
         point_alpha = 0.5) +
  scale_color_manual(values = c("#3d6721", "#a86826", "#006c89")) +
  scale_fill_manual(values = c("#3d6721", "#a86826", "#006c89"))

RIVM-IIV-Microbiome/biomeViz documentation built on July 20, 2022, 3:52 a.m.