plotPairwiseMatrix: Plot pairwise divergence or overlap as calculated by...

In douglasgscofield/dispersalDiversity: Analyse individual and genetic diversity of dispersal processes in biological populations

Description

Plot lower-triangular matrix of pairwise divergence or overlap values using a colour scale and levelplot from the lattice package. The mean value may be included.

Usage

plotPairwiseMatrix(x, statistic = c("divergence", "overlap"),
  pairwise.mean = NULL, mean.position = c(0.45, 0.3), bty = "L",
  aspect = "iso", col.regions = function(x) gray(c(1, seq(0.9, 0.6,
  length.out = (x - 2)), 0)), colorkey = list(labels = list(cex = 1)),
  at = c(0, 0.01, seq(0.2, 0.8, 0.2), 0.99, 1), scales = list(draw = FALSE,
  tck = 0, cex = 0.7, x = list(rot = 90)), axis.label = "Group",
  xlab = list(axis.label, cex = 1), ylab = list(axis.label, cex = 1),
  digits = getOption("digits"), ...)

Arguments

x	Pairwise divergence or overlap matrix as found at, e.g., diversity()$q$diversity.mat. Currently, prior to plotting this matrix has its diagonal and upper triangle zeroed, and is then rotated prior to passing to lattice::levelplot.
statistic	"divergence" or "overlap", indicating the statistic being supplied for plotting
pairwise.mean	Mean pairwise divergence or overlap as found at, e.g., diversity()$q$divergence. If provided, this is added to the plot in the upper triangle, rounded to three digits, with positions specified by mean.pos. The value is plotted together with '\bar{δ} = ' if statistic is "divergence", and '\bar{ω} = ' if statistic is "overlap".
bty, aspect, col.regions, colorkey, at, scales, xlab, ylab	Additional plot options passed to lattice::levelplot
axis.label	Label used for the X and Y axes, the X and Y axis labels can be changed with xlab and ylab
digits	Number of digits to use when printing mean value, taken from the "digits" option if not supplied
mean.pos	If pairwise.mean is given, the relative X and Y positions within the panel at which the value is plotted, in a two-element vector. adj = c(0, 0) is used when plotting the value.

Details

The default colour scheme used is grayscale, with white and black used for values very near the extremes (within 0.01 of 0 and 1, respectively). Options are available for modifying the colour scheme.

Value

The class lattice plot object is returned invisibly

References

Scofield, D. G., Smouse, P. E., Karubian, J. and Sork, V. L. (2012) Use of alpha, beta and gamma diversity measures to characterize seed dispersal by animals. American Naturalist 180:719-732.

See Also

diversity, lattice::levelplot

Examples

data(granaries_2002_Qlob)
d <- diversity(granaries_2002_Qlob)
plotPairwiseMatrix(x = d$r$divergence.mat,
                   pairwise.mean = d$r$divergence,
                   statistic = "divergence",
                   axis.label = "Granary")

douglasgscofield/dispersalDiversity documentation built on March 30, 2021, 9:50 a.m.