plot.comparative.comm: Dot-plots of community presence/absence or abundance

In pez: Phylogenetics for the Environmental Sciences

Dot-plots of community presence/absence or abundance

Description

Dot-plots of community presence/absence or abundance

Usage

## S3 method for class 'comparative.comm'
plot(
  x,
  sites = NULL,
  abundance = FALSE,
  pch = 20,
  dot.cex = NULL,
  site.col = "black",
  fraction = 3,
  x.increment = NULL,
  show.tip.label = FALSE,
  ...
)

Arguments

x	comparative.comm object
sites	names of sites to plot (default: all); see examples
abundance	make size proportional to species abundance (default: FALSE)
pch	plotting character to be used for sites (see pch)
dot.cex	function to determine point size; see examples, this isn't as terrible-sounding as it seems.
site.col	colours to use when plotting sites; if not same length as number of sites, only the first element is used (no recycling)
fraction	fraction of plot window to be taken up with phylogeny; e.g., 3 (default) means phylogeny is 1/3 of plot
x.increment	specify exact spacing of points along plot; see examples
show.tip.label	whether to plot species names on phylogeney (default: FALSE)
...	additional arguments passed to plotting functions

Details

Take a look at the examples: this is (hopefully!) a lot more straightforward than it might seem. Getting the right spacing of dots on the phylogeny may take some playing around with the fraction and x.increment arguments. It may seem a little strange to set point size using a function, however, this gives you much more flexibility and the ability to (usefully) transform your data.

Value

List containing plot.phylo information, as well as the used x.adj values (compare with your x.increment)

Author(s)

Will Pearse, Matt Helmus

See Also

comparative.comm traitgram.cc

Examples

data(laja)
data <- comparative.comm(invert.tree, river.sites, invert.traits)
plot(data)
plot(data, sites=c("AT", "BP"), fraction=1.5)
settings <- plot(data, sites=c("AT", "BP"), site.col=rainbow(2), fraction=1.5)
plot(data, sites=c("AT", "BP"), site.col=rainbow(2),
fraction=1.2, x.increment=settings$x.increment/4)
#dot.cex isn't as scary as it sounds...
plot(data, site.col=rainbow(2), fraction=1.2, abundance=TRUE, dot.cex=sqrt)
#...or other trivial variants...
abund.sqrt <- function(x) ifelse(x>0, sqrt(x), 0)
plot(data, sites=c("AT", "BP"), site.col=rainbow(2), fraction=1.2,
x.increment=settings$x.increment/4, abundance=TRUE, dot.cex=abund.sqrt)
plot(data, sites=c("AT", "BP"), site.col=rainbow(2), fraction=1.2,
x.increment=settings$x.increment/4, abundance=TRUE, dot.cex=function(x) sqrt(x))

pez documentation built on Aug. 29, 2025, 5:33 p.m.