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Minimal plotting system for morphometric shapes

Source: R/p_graphics.R
p.Rd

A collection of functions for creating clean, publication-ready visualizations of morphometric data. The p() function initializes a minimal plot, and draw_* functions add layers. All functions return their input invisibly, enabling pipe-friendly workflows.

Usage

p(x, xlim, ylim, axes = TRUE)

draw_landmarks(x, col = "grey20", pch = 3, cex = 0.25, ...)

draw_landmarks_as_numbers(x, col = "grey20", pch = 3, cex = 0.5, ...)

draw_outlines(x, col = "grey20", lwd = 0.2, ...)

draw_centroid(x, col = "orange", cex = 1/4, pch = 3, ...)

draw_first_point(x, col = "grey20", cex = 1/3, label = "v", ...)

draw_links(x, links, col = "grey20", lwd = 0.5, ...)

Arguments

x

A matrix (single shape) or list of matrices containing (x, y) coordinates

xlim

Numeric vector of length 2 giving x-axis limits. If missing, calculated from data

ylim

Numeric vector of length 2 giving y-axis limits. If missing, calculated from data

axes

Logical. Whether to draw axes.

col

Character. Color for points, lines, or axes

pch

Integer. Point character type

cex

Numeric. Character/point expansion factor

...

Additional graphical parameters passed to underlying functions

lwd

Numeric. Line width

label

Character. Label to display at first point (default: "v")

A two-column matrix where each row defines a segment. First column is the start landmark index, second column is the end landmark index. This matrix is recycled across all shapes in x.

Value

All functions invisibly return x as a list (for piping)

Details

p(): The base plotter function that opens a device, sets up minimal axes with 1:1 aspect ratio, and prepares the plot area.

draw_landmarks(): Adds landmark points to the current plot.

draw_outlines(): Draws outline curves by connecting coordinates with lines.

draw_centroid(): Marks the centroid (mean x, mean y) of each shape.

draw_first_point(): Marks the first point with a rotated label that points from the first toward the second point.

Examples

# Basic plotting
shapes[1] %>% p() %>% draw_outlines()

shapes %>% p() %>% draw_outlines()

# Chaining draw functions
p(shapes) |> draw_outlines() |> draw_centroid()


# With custom styling
p(shapes) |>
  draw_outlines(col = "blue", lwd = 0.5) |>
  draw_centroid(col = "red", cex = 0.5)


# dummy links, mosquito people please have mercy!