plot_heatmap: Heatmap of species abundance matrix

Description Usage Arguments Details Value See Also Examples

Description

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

Usage

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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

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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 Dec. 7, 2018, 6:06 p.m.