Plot and test local contributions to beta diversity (LCBD) of samples

A wrapper for the adespatial::beta.div() function in the case of physeq object.

Usage

plot_LCBD_pq(
  physeq,
  p_adjust_method = "BH",
  pval = 0.05,
  sam_variables = NULL,
  only_plot_significant = TRUE,
  ...
)

Arguments

physeq: (required): a phyloseq-class object obtained using the phyloseq package.
p_adjust_method: (chr, default "BH"): the method used to adjust p-value
pval: (int, default 0.05): the value to determine the significance of LCBD
sam_variables: A vector of variables names present in the sam_data slot to plot alongside the LCBD value
only_plot_significant: (logical, default TRUE) Do we plot all LCBD values or only the significant ones
...: Others arguments passed on to adespatial::beta.div() function

Value

A ggplot2 object build with the package patchwork

Details

This function is mainly a wrapper of the work of others. Please make a reference to vegan::beta.div() if you use this function.

Author

Adrien Taudière

Examples

data(data_fungi)
if (requireNamespace("adespatial")) {
  plot_LCBD_pq(data_fungi_mini,
    nperm = 100, only_plot_significant = FALSE,
    pval = 0.2
  )
}
#> Taxa are now in columns.

# \donttest{
if (requireNamespace("adespatial")) {
  plot_LCBD_pq(data_fungi_mini,
    nperm = 100, only_plot_significant = TRUE,
    pval = 0.2
  )
  if (requireNamespace("patchwork")) {
    plot_LCBD_pq(data_fungi_mini,
      nperm = 100, only_plot_significant = FALSE,
      sam_variables = c("Time", "Height")
    )
    plot_LCBD_pq(data_fungi_mini,
      nperm = 100, only_plot_significant = TRUE, pval = 0.2,
      sam_variables = c("Time", "Height", "Tree_name")
    ) &
      theme(
        legend.key.size = unit(0.4, "cm"),
        legend.text = element_text(size = 10),
        axis.title.x = element_text(size = 6)
      )
  }
}
#> Taxa are now in columns.
#> Taxa are now in columns.
#> Taxa are now in columns.

# }