PCoA plot

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.

Value

a ggplot2 object.

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.

References

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

Author

Sudarshan A. Shetty

Examples

library(biomeUtils)
library(dplyr)
library(ggside)
#> Registered S3 method overwritten by 'ggside':
#>   method from   
#>   +.gg   ggplot2
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"))
#> Random number for permutation analysis ...
#> 1253
#> 'adonis' will be deprecated: use 'adonis2' instead
#> Warning: Second of the choosen axis in `axis_plot` has no taxa satisfying criteria to plot