plot_taxa_ridges: Taxon change point ridge plots

Description

Taxon change point ridge plots

Usage

plot_taxa_ridges(
  titan.out,
  z1 = TRUE,
  z2 = TRUE,
  z1_fill_low = "lightblue",
  z1_fill_high = "black",
  z2_fill_low = "pink",
  z2_fill_high = "red",
  xlabel = "Environmental Gradient",
  n_ytaxa = 90,
  printspp = FALSE,
  grid = TRUE,
  d_lines = FALSE,
  trans = "identity",
  xaxis = !grid,
  xlim,
  breaks = ggplot2::waiver(),
  bw,
  rel_heights,
  ...,
  axis.text.x,
  axis.text.y,
  axis.title.x,
  axis.title.y
)

Value

A plot of decreasing and/or increasing taxon-specific change points along the environmental gradient.

Arguments

titan.out: A TITAN output object.
z1: A logical specifying whether decreasing taxa should be plotted.
z2: A logical specifying whether increasing taxa should be plotted.
z1_fill_low, z1_fill_high, z2_fill_low, z2_fill_high: Respective fill colors passed to ggplot2::scale_fill_gradient()
xlabel: A character string for the x axis label.
n_ytaxa: The maximum number of taxa to be plotted.
printspp: A logical specifying whether the sppmax table should be printed.
grid: The grid argument of ggridges::theme_ridges(). Setting this to FALSE removes horizontal lines from the plot, see examples.
d_lines: Argument to pass to ggridges::geom_density_ridges(). Short for density lines, a logical determining whether the median change point values from estimated from each taxon's density function, is plotted. If TRUE, a dashed, black vertical line will be plotted.
trans: a scale transformation to be applied to the x-axis through ggplot2. e.g. "log10" or "sqrt".
xaxis: Logical; should the x-axis be plotted?
xlim: x axis limits, e.g. xlim = c(0,10).
breaks: Argument to pass to ggridges::geom_density_ridges(). Determines values and labels of breaks (ticks) on the x-axis.
bw: The bandwidth of used in the kernel density estimate; see density().
rel_heights: Argument to pass to cowplot::plot_grid() as an override for the defaults
...: Arguments to pass to ggridges::geom_density_ridges()
axis.text.x, axis.text.y, axis.title.x, axis.title.y: Font sizes of respective axis text. Passed as the size argument to the ggplot2 thematic elements of the same name. Defaults to current default ggplot2 theme.

Author

M. Baker, R. King, D. Kahle

References

Baker, ME and RS King. 2010. A new method for detecting and interpreting biodiversity and ecological community thresholds. Methods in Ecology and Evolution 1(1): 25:37.