Beta diversity plot with multiple distance and ordination methods

Source: R/beta_div_plot.R

This function computes beta diversity using several distance metrics and ordination methods (PCA, PCoA, NMDS). It requires an abundance table with taxonomy, metadata, and allows customization of color and shape aesthetics. It also supports compositional transformation via ALDEx2.

beta_div_plot(
  table,
  metadata,
  distance = "compositional",
  ordination = "PCA",
  group_col = NULL,
  group_colors = NULL,
  shape_col = NULL,
  legend_title = NULL,
  arrows_size = 10,
  top_n = 5
)

Arguments

table

A data frame with abundances. The last column must contain taxonomy information.

metadata

A data frame with sample metadata. The first column must contain the sample IDs.

distance

Distance method: one of "euclidean", "bray", "jaccard", "sorensen", "compositional" (default), "aitchison", or "robust.aitchison".

ordination

Ordination method: one of "PCA" (default), "PCoA", or "NMDS".

group_col

Column in metadata to fill color points.

group_colors

Optional named vector of colors.

shape_col

Optional column in metadata to shape points.

legend_title

Optional legend title.

top_n

Number of top contributing taxa to display as arrows in PCA.

Value

A ggplot2 object.

Examples

     beta_div_plot(table = table_taxa,
                              metadata = metadata1,
                              distance = "aitchison",
                              ordination = "NMDS",
                              group_col  = "SITIO",
                              top_n = 5,
                              arrows = 100)
#> Loading required namespace: ggrepel
#> Error: object 'table_taxa' not found