CCA/RDA Biplot with ggplot2 — cca_rda

Performs Canonical Correspondence Analysis (CCA) or Redundancy Analysis (RDA) based on a species abundance table and selected environmental variables, returning a biplot with ggplot2 that visualizes sample scores and environmental vectors.

cca_rda_biplot(
  table,
  env_data,
  env_vars,
  method = "hell",
  metadata = NULL,
  group_col = NULL,
  group_colors = NULL,
  legend_title = NULL,
  scale_env = TRUE,
  pval_threshold = 0.05,
  show_all_env_vectors = FALSE,
  analysis = "CCA",
  seed = 126,
  scale_arrows = 1,
  title = NULL
)

Arguments

table: A data frame or matrix of species abundances (samples as rows, species as columns).
env_data: A data frame of environmental variables (rows must match table).
env_vars: A character vector with the names of environmental variables to include in the analysis.
method: Transformation method passed to decostand (default is "hell" for Hellinger).
metadata: Optional data frame with sample metadata for grouping in the plot.
group_col: Optional name of the column in metadata used to define sample groups.
group_colors: Optional named vector of colors to use for each group.
legend_title: Optional custom title for the group legend.
scale_env: Logical; whether to scale environmental variables (default is TRUE).
pval_threshold: P-value threshold for selecting significant environmental variables (default is 0.05).
show_all_env_vectors: Logical; if TRUE, plot all environmental vectors regardless of significance.
analysis: Either "CCA" or "RDA" (default is "CCA").
seed: Random seed for reproducibility (default is 126).
scale_arrows: Numeric value to scale environmental vectors in the plot.
title: Optional plot title.

Value

A ggplot object displaying the biplot with sample scores and environmental vectors.

Examples

cca_rda_biplot(table = table,
              env_data = env_data,
              env_vars = c("pH", "Nitrogen", "Calcium"),
              metadata = metadata ,
              group_col = "metodo",
              analysis = "RDA",
              show_all_env_vectors = TRUE,
              legend_title = "Método",
              group_colors = c("red", "blue"),
              title = "title")
#> Loading required package: ggplot2
#> Warning: package 'ggplot2' was built under R version 4.4.3
#> Loading required package: dplyr
#> Warning: package 'dplyr' was built under R version 4.4.3
#> 
#> Attaching package: 'dplyr'
#> The following objects are masked from 'package:stats':
#> 
#>     filter, lag
#> The following objects are masked from 'package:base':
#> 
#>     intersect, setdiff, setequal, union
#> Error in cca_rda_biplot(table = table, env_data = env_data, env_vars = c("pH",     "Nitrogen", "Calcium"), metadata = metadata, group_col = "metodo",     analysis = "RDA", show_all_env_vectors = TRUE, legend_title = "Método",     group_colors = c("red", "blue"), title = "title"): There is no taxonomy column in the table