spaMM.filled.contour: Level (Contour) Plots with better aspect ratio control (for...

In spaMM: Mixed-Effect Models, with or without Spatial Random Effects

Level (Contour) Plots with better aspect ratio control (for geographical maps, at least)

Description

This function is derived from filled.contour in the graphics package, and this documentation is likewise heavily based on that of filled.contour.

This function likewise produces a contour plot with the areas between the contours filled in solid color, and a key showing how the colors map to z values is likewise shown to the right of the plot. The only difference is the way the aspect ratio is determined and can be controlled (using the map.asp parameter instead of asp), They thus easily provide nice-looking maps with meaningful latitude/longitude ratio (see Examples). However, this does not work well with rstudio.

Usage

spaMM.filled.contour(x = seq(0, 1, length.out = nrow(z)),
               y = seq(0, 1, length.out = ncol(z)),
               z,
               xrange = range(x, finite = TRUE),
               yrange = range(y, finite = TRUE),
               zrange = range(z, finite = TRUE, na.rm=TRUE),
               margin=1/20,
               levels = pretty(zrange, nlevels), nlevels = 20,
               color.palette = spaMM.colors,
               col = color.palette(length(levels) - 1),
               plot.title, plot.axes, key.title=NULL, key.axes=NULL,
               map.asp = NULL, xaxs = "i", yaxs = "i", las = 1,
               axes = TRUE, frame.plot = axes, ...)

Arguments

x, y	locations of grid lines at which the values in z are measured. These must be in ascending order. (The rest of this description does not apply to .filled.contour.) By default, equally spaced values from 0 to 1 are used. If x is a list, its components x$x and x$y are used for x and y, respectively. If the list has component z this is used for z.
z	a numeric matrix containing the values to be plotted.. Note that x can be used instead of z for convenience.
xrange	x range of the plot.
yrange	y range of the plot.
zrange	z range of the plot.
margin	This controls how far (in relative terms) the plot extends beyond the x and y ranges of the analyzed points, and is overriden by explicit xrange and yrange arguments.
levels	a set of levels which are used to partition the range of z. Must be strictly increasing (and finite). Areas with z values between consecutive levels are painted with the same color.
nlevels	if levels is not specified, the range of z, values is divided into approximately this many levels.
color.palette	a color palette function to be used to assign colors in the plot.
col	an explicit set of colors to be used in the plot. This argument overrides any palette function specification. There should be one less color than levels
plot.title	statements which add titles to the main plot.
plot.axes	statements which draw axes (and a box) on the main plot. This overrides the default axes.
key.title	statements which add titles for the plot key.
key.axes	statements which draw axes on the plot key. This overrides the default axis.
map.asp	the y/x aspect ratio of the 2D plot area (not of the full figure including the scale). Default is (plotted y range)/(plotted x range) (i.e., scales for x are identical).
xaxs	the x axis style. The default is to use internal labeling.
yaxs	the y axis style. The default is to use internal labeling.
las	the style of labeling to be used. The default is to use horizontal labeling.
axes, frame.plot	logicals indicating if axes and a box should be drawn, as in plot.default.
...	additional graphical parameters, currently only passed to title().

Details

The values to be plotted can contain NAs. Rectangles with two or more corner values are NA are omitted entirely: where there is a single NA value the triangle opposite the NA is omitted.

Values to be plotted can be infinite: the effect is similar to that described for NA values.

Value

This returns invisibly a list with elements of the plot, the x, y, z coordinates and the contour levels.

Note

Builds heavily on filled.contour by Ross Ihaka and R-core. spaMM.filled.contour uses the layout function and so is restricted to a full page display.

The output produced by spaMM.filled.contour is actually a combination of two plots; one is the filled contour and one is the legend. Two separate coordinate systems are set up for these two plots, but they are only used internally – once the function has returned these coordinate systems are lost. If you want to annotate the main contour plot, for example to add points, you can specify graphics commands in the plot.axes argument. See the Examples.

References

Cleveland, W. S. (1993) Visualizing Data. Summit, New Jersey: Hobart.

See Also

contour, image, palette; contourplot and levelplot from package lattice.

Examples

spaMM.filled.contour(volcano, color.palette = spaMM.colors) # simple

## Comparing the layout with that of filled.contour:
#  (except that it does not always achieve the intended effect 
#  in RStudio Plots pane). 

x <- 10*1:nrow(volcano)
y <- 10*1:ncol(volcano)
spaMM.filled.contour(x, y, volcano, color.palette = terrain.colors,
    plot.title = title(main = "The Topography of Maunga Whau",
    xlab = "Meters North", ylab = "Meters West"),
    plot.axes = { axis(1, seq(100, 800, by = 100))
                  axis(2, seq(100, 600, by = 100)) },
    key.title = title(main = "Height\n(meters)"),
    key.axes = axis(4, seq(90, 190, by = 10)))  # maybe also asp = 1
mtext(paste("spaMM.filled.contour(.) from", R.version.string),
      side = 1, line = 4, adj = 1, cex = .66)

## compare with      

filled.contour(x, y, volcano, color.palette = terrain.colors,
    plot.title = title(main = "The Topography of Maunga Whau",
    xlab = "Meters North", ylab = "Meters West"),
    plot.axes = { axis(1, seq(100, 800, by = 100))
                  axis(2, seq(100, 600, by = 100)) },
    key.title = title(main = "Height\n(meters)"),
    key.axes = axis(4, seq(90, 190, by = 10)))  # maybe also asp = 1
mtext(paste("filled.contour(.) from", R.version.string),
      side = 1, line = 4, adj = 1, cex = .66)

spaMM documentation built on June 22, 2024, 9:48 a.m.