Skip to contents

Plot a nicheR ellipsoid in environmental space

Source: R/plot_utilities.R
plot_ellipsoid.Rd

Plots the 2D boundary of a nicheR_ellipsoid object in environmental space for a chosen pair of dimensions. Optionally overlays background points or a prediction surface colored by a continuous variable (e.g., suitability). Use add_data and add_ellipsoid to layer additional data onto the plot after calling this function.

Usage

plot_ellipsoid(object, background = NULL, prediction = NULL,
               dim = c(1, 2), col_layer = NULL,
               pal = hcl.colors(100, palette = "Viridis"), rev_pal = FALSE,
               bg_sample = NULL,
               lty = 1, lwd = 1, col_ell = "#000000",col_bg = "#8A8A8A",
               pch = 1, alpha_bg = 1, alpha_ell = 1,
               cex_ell = 1, cex_bg = 1,
               fixed_lims = NULL,...)

Arguments

object

A nicheR_ellipsoid object containing at least centroid, cov_matrix, chi2_cutoff, and var_names.

background

Optional data frame or matrix of background points to plot behind the ellipsoid. Rows are observations, columns are environmental variables. If provided, prediction is ignored.

prediction

Optional data frame or matrix of prediction values to plot. Used when background is NULL. Can be colored by a continuous variable using col_layer.

dim

Integer vector of length 2. Indices of the two dimensions to plot. Default is c(1, 2).

col_layer

Character or NULL. Name of a column in prediction to use for coloring points by a continuous variable. If NULL (default), all prediction points are drawn with col_bg.

pal

A color palette function or character vector used when col_layer is provided. Default is hcl.colors(100, palette = "Viridis").

rev_pal

Logical. If TRUE, reverses the color palette. Default is FALSE.

bg_sample

Integer or NULL. If provided and the number of background or prediction rows exceeds this value, a random subsample of this size is drawn before plotting. Useful for large data frames. Default is NULL (plot all points).

lty

Integer. Line type for the ellipsoid boundary. Default is 1 (solid).

lwd

Numeric. Line width for the ellipsoid boundary. Default is 1.

col_ell

Character. Color of the ellipsoid boundary line. Default is "#000000" (black).

col_bg

Character. Color of background or prediction points when col_layer is NULL. Default is "#8A8A8A" (grey).

pch

Integer or character. Point symbol for background or prediction points. Default is 1.

alpha_bg

Numeric in [0, 1]. Transparency of background or prediction points. Default is 1 (fully opaque).

alpha_ell

Numeric in [0, 1]. Transparency of the ellipsoid boundary line. Default is 1 (fully opaque).

cex_ell

Numeric. Size scaling for the ellipsoid boundary line. Default is 1.

cex_bg

Numeric. Size scaling for background or prediction points. Default is 1.

fixed_lims

A named list with elements xlim and ylim, each a numeric vector of length 2. When provided, overrides the limits computed by safe_lims(). Intended for use by plot_ellipsoid_pairs to enforce consistent axis scales across panels, but can also be set manually by the user. Default is NULL (limits computed from data).

...

Additional graphical parameters passed to plot.

Value

Called for its side effect of creating a plot. Returns NULL invisibly.

Details

The function has three display modes depending on what is provided:

  1. Background only (background is not NULL): plots background points in col_bg with the ellipsoid boundary overlaid.

  2. Prediction surface (background is NULL, prediction is not NULL): plots prediction points, optionally colored by col_layer using values mapped onto pal. When col_layer is provided, points outside the ellipsoid (zero or NA in col_layer, as produced by truncated prediction types) are drawn in col_bg behind the colored interior points. Axis limits are computed from the full prediction extent so the view is never collapsed to the ellipsoid interior.

  3. Ellipsoid only (both NULL): plots the ellipsoid boundary alone with no background.

See also

add_data to overlay occurrence points, add_ellipsoid to overlay additional ellipsoid boundaries, plot_ellipsoid_pairs for pairwise plots of all dimensions vignette("plotting_vignette", package = "nicheR")

Examples

data("ref_ellipse", package = "nicheR")
data("back_data", package = "nicheR")

# Mode 1: ellipsoid boundary only
plot_ellipsoid(ref_ellipse,
               col_ell = "#e10000", lwd = 2,
               xlab = "Bio1 (Mean Annual Temperature)",
               ylab = "Bio12 (Annual Precipitation)")


# Mode 2: with background points
plot_ellipsoid(ref_ellipse,
               background = back_data,
               col_ell = "#e10000", col_bg = "grey70",
               lwd = 2, pch = 20, cex_bg = 0.4,
               xlab = "Bio1", ylab = "Bio12")


# Mode 3: prediction colored by suitability
pred_df <- utils::read.csv(system.file("extdata", "predictions_virt.csv", package = "nicheR"))

plot_ellipsoid(ref_ellipse,
               prediction = pred_df,
               col_layer = "suitability",
               bg_sample = 1000,
               col_ell = "#e10000", lwd = 2,
               pch = 20, cex_bg = 0.4,
               xlab = "Bio1", ylab = "Bio12")


# Mode 3b: truncated suitability, outside points shown in grey
plot_ellipsoid(ref_ellipse,
               prediction = pred_df,
               col_layer = "suitability_trunc",
               col_bg  = "#d4d4d4",
               col_ell = "#e10000", lwd = 2, pch = 20, cex_bg = 0.4,
               xlab = "Bio1", ylab = "Bio12")