This is just the ape::plot.phylo method, which is imported and exported directly by the nodiv package. These functions plot phylogenetic trees on the current graphical device.
phyplot(x, type = "phylogram", use.edge.length = TRUE,
node.pos = NULL, show.tip.label = TRUE, show.node.label = FALSE,
edge.color = "black", edge.width = 1, edge.lty = 1, font = 3,
cex = par("cex"), adj = NULL, srt = 0, no.margin = FALSE,
root.edge = FALSE, label.offset = 0, underscore = FALSE,
x.lim = NULL, y.lim = NULL, direction = "rightwards",
lab4ut = NULL, tip.color = "black", plot = TRUE,
rotate.tree = 0, open.angle = 0, node.depth = 1, align.tip.label = FALSE, ...)plot.phylo returns invisibly a list with the following
components which values are those used for the current plot:
an object of class "phylo"
a character string specifying the type of phylogeny to be drawn; it must be one of "phylogram" (the default), "cladogram", "fan", "unrooted", "radial" or any unambiguous abbreviation of these.
a logical indicating whether to use the edge
lengths of the phylogeny to draw the branches (the default) or not
(if FALSE). This option has no effect if the object of class
"phylo" has no `edge.length' element.
a numeric taking the value 1 or 2 which specifies the
vertical position of the nodes with respect to their descendants. If
NULL (the default), then the value is determined in relation
to `type' and `use.edge.length' (see details).
a logical indicating whether to show the tip
labels on the phylogeny (defaults to TRUE, i.e. the labels
are shown).
a logical indicating whether to show the node
labels on the phylogeny (defaults to FALSE, i.e. the labels
are not shown).
a vector of mode character giving the colours used
to draw the branches of the plotted phylogeny. These are taken to be
in the same order than the component edge of phy. If
fewer colours are given than the length of edge, then the
colours are recycled.
a numeric vector giving the width of the branches of
the plotted phylogeny. These are taken to be in the same order than
the component edge of phy. If fewer widths are given
than the length of edge, then these are recycled.
same than the previous argument but for line types; 1: plain, 2: dashed, 3: dotted, 4: dotdash, 5: longdash, 6: twodash.
an integer specifying the type of font for the labels: 1 (plain text), 2 (bold), 3 (italic, the default), or 4 (bold italic).
a numeric value giving the factor scaling of the tip and node labels (Character EXpansion). The default is to take the current value from the graphical parameters.
a numeric specifying the justification of the text strings
of the labels: 0 (left-justification), 0.5 (centering), or 1
(right-justification). This option has no effect if type =
"unrooted". If NULL (the default) the value is set with
respect of direction (see details).
a numeric giving how much the labels are rotated in degrees
(negative values are allowed resulting in clock-like rotation); the
value has an effect respectively to the value of
direction (see Examples). This option has no effect if
type = "unrooted".
a logical. If TRUE, the margins are set to
zero and the plot uses all the space of the device (note that this
was the behaviour of plot.phylo up to version 0.2-1 of `ape'
with no way to modify it by the user, at least easily).
a logical indicating whether to draw the root edge (defaults to FALSE); this has no effect if `use.edge.length = FALSE' or if `type = "unrooted"'.
a numeric giving the space between the nodes and
the tips of the phylogeny and their corresponding labels. This
option has no effect if type = "unrooted".
a logical specifying whether the underscores in tip
labels should be written as spaces (the default) or left as are (if
TRUE).
a numeric vector of length one or two giving the limit(s)
of the x-axis. If NULL, this is computed with respect to
various parameters such as the string lengths of the labels and the
branch lengths. If a single value is given, this is taken as the
upper limit.
same than above for the y-axis.
a character string specifying the direction of the tree. Four values are possible: "rightwards" (the default), "leftwards", "upwards", and "downwards".
(= labels for unrooted trees) a character string
specifying the display of tip labels for unrooted trees (can be
abbreviated): either "horizontal" where all labels are
horizontal (the default if type = "u"), or "axial"
where the labels are displayed in the axis of the corresponding
terminal branches. This option has an effect if type = "u",
"f", or "r".
the colours used for the tip labels, eventually recycled (see examples).
a logical controlling whether to draw the tree. If
FALSE, the graphical device is set as if the tree was
plotted, and the coordinates are saved as well.
for "fan", "unrooted", or "radial" trees: the rotation of the whole tree in degrees (negative values are accepted).
if type = "f" or "r", the angle in
degrees left blank. Use a non-zero value if you want to call
axisPhylo after the tree is plotted.
an integer value (1 or 2) used if branch lengths are not used to plot the tree; 1: the node depths are proportional to the number of tips descending from each node (the default and was the only possibility previously), 2: they are evenly spaced.
a logical value or an integer. If TRUE, the tips are aligned and dotted lines are drawn between the tips of the tree and the labels. If an integer, the tips are aligned and this gives the type of the lines (lty).
further arguments to be passed to plot or to
plot.phylo.
Emmanuel Paradis
The font format of the labels of the nodes and the tips is the same.
If no.margin = TRUE, the margins are set to zero and are not
restored after plotting the tree, so that the user can access the
coordinates system of the plot.
The option `node.pos' allows the user to alter the vertical position
(i.e., ordinates) of the nodes. If node.pos = 1, then the
ordinate of a node is the mean of the ordinates of its direct
descendants (nodes and/or tips). If node.pos = 2, then the
ordinate of a node is the mean of the ordinates of all the tips of
which it is the ancestor. If node.pos = NULL (the default),
then its value is determined with respect to other options: if
type = "phylogram" then `node.pos = 1'; if type =
"cladogram" and use.edge.length = FALSE then `node.pos = 2';
if type = "cladogram" and use.edge.length = TRUE then
`node.pos = 1'. Remember that in this last situation, the branch
lengths make sense when projected on the x-axis.
If adj is not specified, then the value is determined with
respect to direction: if direction = "leftwards" then
adj = 1 (0 otherwise).
If the arguments x.lim and y.lim are not specified by the
user, they are determined roughly by the function. This may not always
give a nice result: the user may check these values with the
(invisibly) returned list (see ``Value:'').
If you resize manually the graphical device (windows or X11) you may need to replot the tree.
plot.phylo