plot_heatmap: Heatmap of species abundance matrix

In phytomosaic/ecole: ecole: School of Ecology Package

Description

Plot site x species matrix with heatmap colors and proper labels.

Usage

plot_heatmap(
  x,
  xord = "none",
  yord = "none",
  logbase = FALSE,
  labcex = 0.7,
  col,
  xexp = 1,
  yexp = 1,
  ...
)

Arguments

x	array of species data, where rows = SUs and cols = species
xord	logical, order columns by species weighted averages?
yord	logical, order rows by species (unweighted) averages?
logbase	numeric, logarithm base to scale plot contrast
labcex	numeric, label expansion factor; defaults to 0.7
col	vector defining a color palette
xexp, yexp	expansion factor making room for x,y labels
...	further arguments passed to other methods

Details

Plots a heatmap to quickly visualize species abundances/occurences.

Value

None, plots to device.

See Also

tabasco for comparison.

Examples

data(smoky)
z <- smoky$spe
# basic
plot_heatmap(z)

# pretty
r <- colorRampPalette(c('transparent','darkgreen'))(99)
plot_heatmap(z, yexp=1.7, logbase=10, asp=1, col=r)

# various ways to order
plot_heatmap(z, xord='wa', yord='none')
plot_heatmap(z, xord='mean', yord='none')
plot_heatmap(z, xord='wa', yord='wa')

phytomosaic/ecole documentation built on Jan. 2, 2022, 11:24 p.m.