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Plot Environmental Bins (2D Projection)

Source: R/plot_env_bins.R
plot_env_bins.Rd

Visualize the output of get_env_bins() by plotting environmental blocks (bins) along two selected environmental variables. Each block is shown as a colored rectangle, and points falling inside the same rectangle share the same block_id.

Usage

plot_env_bins(
  env_bins,
  x_var,
  y_var,
  alpha_blocks = 0.3,
  color_points = "black",
  size_points = 2,
  alpha_points = 0.5,
  stroke_points = 1,
  xlab = NULL,
  ylab = NULL,
  theme_plot = ggplot2::theme_minimal()
)

Arguments

env_bins

(list) output list from get_env_bins(). Must contain:

  • data: data.frame with environmental values, bin indices, and block_id

  • breaks: named list with breakpoints for each variable

x_var

(character) name of the environmental variable used on the x-axis.

y_var

(character) name of the environmental variable used on the y-axis.

alpha_blocks

(numeric) transparency level of the block rectangles. Must be between 0 and 1. Default is 0.3.

color_points

(character) color of the points representing occurrence records. Default is "black".

size_points

(numeric) size of the points representing occurrence records. Default is 2.

alpha_points

(numeric) transparency level of the points. Must be between 0 and 1. Default is 0.5..

stroke_points

(numeric) size of the border of the points. Default is 1.

xlab

(character) label for the x-axis. Default is NULL, meaning the name provided in x_var will be used.

ylab

(character) label for the y-axis. Default is NULL, meaning the name provided in y_var will be used.

theme_plot

(theme) a ggplot2 theme object. Default is ggplot2::theme_minimal().

Value

A ggplot object showing the environmental blocks (colored rectangles) and the occurrence records in the selected environmental space.

Examples

# Load example data
data("occurrences", package = "RuHere")
# Get only occurrences from Araucaria
occ <- occurrences[occurrences$species == "Araucaria angustifolia", ]
# Load example of raster variables
data("worldclim", package = "RuHere")
# Unwrap Packed raster
r <- terra::unwrap(worldclim)
# Get bins
b <- get_env_bins(occ = occ, env_layers = r, n_bins = 10)
# Plot
plot_env_bins(b, x_var = "bio_1", y_var = "bio_12",
              xlab = "Temperature", ylab = "Precipitation")
#> Warning: Removed 147 rows containing missing values or values outside the scale range
#> (`geom_point()`).