plot.correlogram

plot.correlogramList

an object of class <code>"correlogram"</code> or of class
    <code>"correlogramList"</code> (both produced by
    <code><a rd-options="" href="/link/correlogram.formula?package=ape&version=4.0" data-mini-rdoc="ape::correlogram.formula">correlogram.formula</a></code>).

legend

the level used to discriminate the plotting symbols
    with colours considering the P-values.

test.level

two colours for the plotting symbols: the first one is used
    if the P-value is greater than or equal to <code>test.level</code>, the
    second one otherwise.

the type of plot to produce (see
    <code><a rd-options="graphics" href="/link/plot?package=ape&version=4.0&to=graphics" data-mini-rdoc="graphics::plot">plot</a></code> for possible choices).

type

an optional character string for the label on the x-axis
    (none by default).

xlab

ylab

the default size for the plotting symbols.

when plotting several correlograms, should they be
    plotted in trellis-style with lattice (the default), or together on
    the same plot?

lattice

other parameters passed to the <code>plot</code> or <code>lines</code>
    function.


  These functions plot correlagrams previously computed with
  <code><a rd-options="" href="/link/correlogram.formula?package=ape&version=4.0" data-mini-rdoc="ape::correlogram.formula">correlogram.formula</a></code>.


hplot

Functions for reading, writing, plotting, and manipulating phylogenetic trees, analyses of comparative data in a phylogenetic framework, ancestral character analyses, analyses of diversification and macroevolution, computing distances from DNA sequences, reading and writing nucleotide sequences as well as importing from BioConductor, and several tools such as Mantel's test, generalized skyline plots, graphical exploration of phylogenetic data (alex, trex, kronoviz), estimation of absolute evolutionary rates and clock-like trees using mean path lengths and penalized likelihood, dating trees with non-contemporaneous sequences, translating DNA into AA sequences, and assessing sequence alignments. Phylogeny estimation can be done with the NJ, BIONJ, ME, MVR, SDM, and triangle methods, and several methods handling incomplete distance matrices (NJ*, BIONJ*, MVR*, and the corresponding triangle method). Some functions call external applications (PhyML, Clustal, T-Coffee, Muscle, MAFFT) whose results are returned into R.

Emmanuel Paradis

Analyses of Phylogenetics and Evolution

plot.correlogram function

an object of class <code>"correlogram"</code> or of class
    <code>"correlogramList"</code> (both produced by
    <code><a rd-options='' href='correlogram.formula'>correlogram.formula</a></code>).

the type of plot to produce (see
    <code><a rd-options='graphics' href='plot'>plot</a></code> for possible choices).


  These functions plot correlagrams previously computed with
  <code><a rd-options='' href='correlogram.formula'>correlogram.formula</a></code>.


plot.correlogram: Plot a Correlogram

Description

Usage

Arguments

Details

See Also