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Rank Plot

Source: R/AllGenerics.R, R/plot_rank.R
plot_rank.Rd

Plots a rank vs relative abundance diagram.

Usage

plot_rank(object, ...)

# S4 method for matrix
plot_rank(
  object,
  log = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  panel.first = NULL,
  panel.last = NULL,
  legend = list(x = "topright"),
  ...
)

# S4 method for data.frame
plot_rank(
  object,
  log = NULL,
  main = NULL,
  sub = NULL,
  ann = graphics::par("ann"),
  axes = TRUE,
  frame.plot = axes,
  panel.first = NULL,
  panel.last = NULL,
  legend = list(x = "topright"),
  ...
)

Arguments

object

A \(m \times p\) numeric matrix or data.frame of count data (absolute frequencies giving the number of individuals for each category, i.e. a contingency table). A data.frame will be coerced to a numeric matrix via data.matrix().

...

Further graphical parameters.

log

A character string which contains "x" if the x axis is to be logarithmic, "y" if the y axis is to be logarithmic and "xy" or "yx" if both axes are to be logarithmic (base 10).

main

A character string giving a main title for the plot.

sub

A character string giving a subtitle for the plot.

ann

A logical scalar: should the default annotation (title and x, y and z axis labels) appear on the plot?

axes

A logical scalar: should axes be drawn on the plot?

frame.plot

A logical scalar: should a box be drawn around the plot?

panel.first

An an expression to be evaluated after the plot axes are set up but before any plotting takes place. This can be useful for drawing background grids.

panel.last

An expression to be evaluated after plotting has taken place but before the axes, title and box are added.

legend

A list of additional arguments to be passed to graphics::legend(); names of the list are used as argument names. If NULL, no legend is displayed.

Value

plot_rank() is called it for its side-effects: it results in a graphic being displayed (invisibly returns object).

References

Magurran, A. E. (1988). Ecological Diversity and its Measurement. Princeton, NJ: Princeton University Press. doi:10.1007/978-94-015-7358-0 .

See also

Other plot methods: matrigraph(), plot_bertin(), plot_diceleraas(), plot_diversity, plot_ford(), plot_heatmap(), plot_rarefaction, plot_spot(), seriograph()

Author

N. Frerebeau

Examples

## Data from Conkey 1980, Kintigh 1989
data("cantabria")

## Plot rank vs abundance
plot_rank(cantabria)


## Change graphical parameters
col <- khroma::color("bright")(5)
plot_rank(cantabria, col = col, pch = 15:19, lty = 2)