magicaxis: Pretty Scientific Plotting

Overview

magicaxis provides functions for making pretty, publication-quality scientific plots with base R graphics. It handles minor tick marks, log-scale axes, 2-D density contours, image display, hexagonal binning, and triangle (corner) plots for MCMC chains.

Since version 2.5.3, all internal argument dispatch uses ParmOff instead of do.call. This lets extra ... arguments be forwarded flexibly to each sub-function: unrecognised arguments are silently dropped, so callers no longer need to know exactly which parameters each inner function accepts.

magaxis – pretty axis labelling

magaxis() adds nicely formatted tick marks and labels to an existing plot. It supports log axes, minor ticks, Hershey fonts, and grid lines.

plot(10^(1:9), 1:9, log = "x", axes = FALSE, xlab = "", ylab = "")
magaxis(side = 1:2, xlab = "x (log scale)", ylab = "y")

Styling arguments such as cex.axis and col.axis are forwarded via ParmOff to the underlying axis() call, while cex.lab and col.lab go to mtext():

plot(1:10, (1:10)^2, axes = FALSE, xlab = "", ylab = "")
magaxis(side = 1:2,
        xlab = "x", ylab = expression(x^2),
        cex.axis = 0.8, col.axis = "steelblue",
        cex.lab  = 1.1, col.lab  = "darkred")

Grid lines can be toggled per axis:

plot(1:20, rnorm(20), axes = FALSE, xlab = "", ylab = "")
magaxis(side = 1:2, grid = TRUE, grid.col = "grey80", grid.lty = 2,
        xlab = "Index", ylab = "Value")

magplot – high-level scatter plots

magplot() wraps plot() to produce pretty axes automatically. For a simple scatter the axis labelling, grid, and limits are handled internally:

x <- 10^(1:9)
y <- 1:9
magplot(log10(x), y, unlog = "x", xlab = "x", ylab = "y")

Log axes on both sides:

magplot(x, y, log = "x", xlab = "x", ylab = "y")

Sigma-clipping the axis limits to focus on where the data actually are:

temp <- cbind(rt(500, df = 1.5), rt(500, df = 1.5))
magplot(temp, xlim = 2, ylim = 2, xlab = "x", ylab = "y",
        main = "2-sigma clipped")

n <- 300
x <- rnorm(n); y <- rnorm(n); z <- x^2 + y^2
magplot(x, y, z = z, xlab = "x", ylab = "y",
        zcol = hcl.colors(21, "YlOrRd"), dobar = TRUE)

maghist – histogram with statistics

maghist() prints a summary and draws a styled histogram. It integrates naturally with magplot() because it returns a histogram object that magplot() detects:

maghist(rnorm(1000), xlab = "Value", verbose = FALSE)

Log-y histogram:

maghist(rnorm(1e4), log = "y", grid = TRUE, verbose = FALSE,
        xlab = "Value", ylab = "Count (log)")

Pass the returned object back through magplot():

h <- maghist(10^runif(500, 0, 3), log = "x", verbose = FALSE)

magplot(h, log = "y", xlab = "x (log)", ylab = "Count (log)")

magcon – 2-D density contours

magcon() computes a 2-D kernel density estimate and draws contours at chosen probability levels (default 50%, 68%, 95%) together with an optional image and colour bar.

x <- rnorm(500); y <- x + rnorm(500, sd = 0.5)
magcon(x, y, h = c(0.2, 0.2), xlab = "x", ylab = "y", barposition = 'topleft',
       bartitleshift = 0.5)
#> Warning in rgl.init(initValue, onlyNULL): X11 error: GLXBadContext
#> Warning: 'rgl.init' failed, will use the null device.
#> See '?rgl.useNULL' for ways to avoid this warning.
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values

Contours only (no background image):

magcon(x, y, h = c(0.2, 0.2), doim = FALSE, dobar = FALSE,
       xlab = "x", ylab = "y")
#> Warning in regularize.values(x, y, ties, missing(ties), na.rm = na.rm):
#> collapsing to unique 'x' values

magbin – 2-D binning

magbin() bins 2-D data into hexagons, squares, or triangles and colours them by count or a user-supplied statistic:

xy <- cbind(rnorm(2000), rnorm(2000))
magbin(xy, shape = "hexagon", xlab = "x", ylab = "y")

Square bins with a z-statistic:

magbin(xy, shape = "square",
       z = xy[, 1]^2 - xy[, 2]^2,
       colref = "zstat", sizeref = "count",
       xlab = "x", ylab = "y")

Log-log hexagonal bins:

xylog <- cbind(10^rnorm(2000), 10^rnorm(2000))
magbin(xylog, log = "xy", xlab = "x (log)", ylab = "y (log)")

magimage – image display

magimage() displays a matrix as an image with a colour map applied via magmap() and optional axes via magaxis(). The internal image() call is dispatched through ParmOff:

z <- outer(seq(-3, 3, len = 50), seq(-3, 3, len = 50),
           function(x, y) exp(-(x^2 + y^2)))
magimage(z, xlab = "x", ylab = "y")

Asinh stretch to reveal faint structure (the default stretch = "asinh" is well suited to images with a wide dynamic range):

z2 <- outer(seq(-3, 3, len = 50), seq(-3, 3, len = 50),
            function(x, y) exp(-x^2) + 0.05 * exp(-y^2 / 0.1))
magimage(z2, stretch = "asinh", xlab = "x", ylab = "y")

magtri – triangle (corner) plots for MCMC chains

magtri() makes a triangle plot summarising posterior samples. The diagonal shows marginal densities, the lower triangle shows 2-D density contours (magcon), and the upper triangle shows scatter plots.

chains <- data.frame(
  alpha = rnorm(500, mean =  1, sd = 0.3),
  beta  = rnorm(500, mean = -0.5, sd = 0.5),
  gamma = rnorm(500, mean =  2,   sd = 0.8)
)
magtri(chains, samples = 300)

# cex.axis → magaxis (tick-label size)
# lty      → magcon  (overrides contour line types)
# col      → points  (overrides the red mean-marker colour)
magtri(chains,
       samples  = 300,
       cex.axis = 0.7,
       lty      = c(2, 1, 3),
       col      = "purple")

magtri(chains,
       samples = 300,
       refvals = c(1, -0.5, 2))

magtri(chains,
       samples = 300,
       refvals = c(1, -0.5, 2),
       majorn = 2)

magtri(chains,
       samples = 300,
       lab = list(
         expression(alpha),
         expression(beta),
         expression(gamma)
       ))