ape: plot.correlogram – R documentation

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ape

plot.correlogram

Plot a Correlogram

Description

These functions plot correlagrams previously computed with correlogram.formula.

Usage

## S3 method for class 'correlogram'
plot(x, legend = TRUE, test.level = 0.05,
                col = c("grey", "red"), type = "b", xlab = "",
                ylab = "Moran's I", pch = 21, cex = 2, ...)
  ## S3 method for class 'correlogramList'
plot(x, lattice = TRUE, legend = TRUE,
                test.level = 0.05, col = c("grey", "red"),
                xlab = "", ylab = "Moran's I",
                type = "b", pch = 21, cex = 2, ...)

Arguments

`x`	an object of class `"correlogram"` or of class `"correlogramList"` (both produced by `correlogram.formula`).
`legend`	should a legend be added on the plot?
`test.level`	the level used to discriminate the plotting symbols with colours considering the P-values.
`col`	two colours for the plotting symbols: the first one is used if the P-value is greater than or equal to `test.level`, the second one otherwise.
`type`	the type of plot to produce (see `plot` for possible choices).
`xlab`	an optional character string for the label on the x-axis (none by default).
`ylab`	the default label on the y-axis.
`pch`	the type of plotting symbol.
`cex`	the default size for the plotting symbols.
`lattice`	when plotting several correlograms, should they be plotted in trellis-style with lattice (the default), or together on the same plot?
`...`	other parameters passed to the `plot` or `lines` function.

Details

When plotting several correlograms with lattice, some options have no effect: legend, type, and pch (pch=19 is always used in this situation).

When using pch between 1 and 20 (i.e., non-filled symbols, the colours specified in col are also used for the lines joining the points. To keep black lines, it is better to leave pch between 21 and 25.

Author(s)

Emmanuel Paradis

Emmanuel Paradis [aut, cre, cph] (<https://orcid.org/0000-0003-3092-2199>), Simon Blomberg [aut, cph] (<https://orcid.org/0000-0003-1062-0839>), Ben Bolker [aut, cph] (<https://orcid.org/0000-0002-2127-0443>), Joseph Brown [aut, cph] (<https://orcid.org/0000-0002-3835-8062>), Santiago Claramunt [aut, cph] (<https://orcid.org/0000-0002-8926-5974>), Julien Claude [aut, cph] (<https://orcid.org/0000-0002-9267-1228>), Hoa Sien Cuong [aut, cph], Richard Desper [aut, cph], Gilles Didier [aut, cph] (<https://orcid.org/0000-0003-0596-9112>), Benoit Durand [aut, cph], Julien Dutheil [aut, cph] (<https://orcid.org/0000-0001-7753-4121>), RJ Ewing [aut, cph], Olivier Gascuel [aut, cph], Thomas Guillerme [aut, cph] (<https://orcid.org/0000-0003-4325-1275>), Christoph Heibl [aut, cph] (<https://orcid.org/0000-0002-7655-3299>), Anthony Ives [aut, cph] (<https://orcid.org/0000-0001-9375-9523>), Bradley Jones [aut, cph] (<https://orcid.org/0000-0003-4498-1069>), Franz Krah [aut, cph] (<https://orcid.org/0000-0001-7866-7508>), Daniel Lawson [aut, cph] (<https://orcid.org/0000-0002-5311-6213>), Vincent Lefort [aut, cph], Pierre Legendre [aut, cph] (<https://orcid.org/0000-0002-3838-3305>), Jim Lemon [aut, cph], Guillaume Louvel [aut, cph] (<https://orcid.org/0000-0002-7745-0785>), Eric Marcon [aut, cph] (<https://orcid.org/0000-0002-5249-321X>), Rosemary McCloskey [aut, cph] (<https://orcid.org/0000-0002-9772-8553>), Johan Nylander [aut, cph], Rainer Opgen-Rhein [aut, cph], Andrei-Alin Popescu [aut, cph], Manuela Royer-Carenzi [aut, cph], Klaus Schliep [aut, cph] (<https://orcid.org/0000-0003-2941-0161>), Korbinian Strimmer [aut, cph] (<https://orcid.org/0000-0001-7917-2056>), Damien de Vienne [aut, cph] (<https://orcid.org/0000-0001-9532-5251>)

Initial release

2021-04-24