Graphical representation of a dissimilarity tree

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Description

Functions to generate a "dot" file and associated images files that can be used in GraphViz to get a graphical representation of the tree.

Usage

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disstree2dot(tree, filename, digits=3, imagefunc=NULL, imagedata=NULL,
            imgLeafOnly=FALSE, devicefunc="jpeg", imageext="jpg",
            device.arg=list(), use.title=TRUE, label.loc="main",
            node.loc="main", split.loc="sub", title.cex=1, legendtext=NULL,
            legendimage=NULL, qualityimage=NULL, showdepth=FALSE,
            title.outer=FALSE, ...)

disstree2dotp(tree, filename, imagedata=NULL, imgLeafOnly=FALSE,
            imagefunc=plot, title.cex=3, withquality=TRUE,
            quality.fontsize=title.cex, title.outer=FALSE, ...)

seqtree2dot(tree, filename, seqdata=tree$info$object, imgLeafOnly=FALSE,
            sortv=NULL, dist.matrix=NULL, title.cex=3, withlegend="auto",
            legend.fontsize=title.cex, withquality=FALSE,
            quality.fontsize=title.cex, axes=FALSE, ...)

Arguments

tree

The tree to be plotted.

filename

A filename, without extension, that will be used to generate image and dot files.

digits

Number of significant digits to plot.

imagefunc

A function to plot the individuals in a node, see details.

imagedata

a data.frame that will be passed to imagefunc, see details.

imgLeafOnly

Logical: If TRUE, only terminal node will be plotted.

devicefunc

A device function, "jpeg" by default.

imageext

extension for image files.

device.arg

Argument passed to devicefunc.

use.title

Logical: If TRUE, node information will be printed using title command, see details.

label.loc

Location of the node label, see title for possible values.

node.loc

Node content location, see title for possible values.

split.loc

Split information location, see title for possible values.

title.cex

cex applied to all calls to title (see use.title).

title.outer

Logical: If TRUE, the title (see use.title) is printed in the outer margins.

legendtext

An optional text appearing in a distinct node.

legendimage

An optional image file appearing in a distinct node.

qualityimage

An optional image file appearing in a distinct node.

showdepth

Logical. If TRUE, information about depth of the tree is added to the plot.

withquality

If TRUE, a node displaying fitting measures of the tree is added to the plot.

quality.fontsize

Numeric. Size of the font of the fitting measures node.

seqdata

a sequence object as defined by the the seqdef function.

sortv

The name of an optional variable used to sort the data before plotting, see seqplot.

dist.matrix

The name of an optional dissimilarity matrix used to find representative sequences, seqrplot.

withlegend

defines if and where the legend of the state colors is plotted. The default value "auto" sets the position of the legend automatically. Other possible value is "right". Obsolete value TRUE is equivalent to "auto".

legend.fontsize

Size of the font of the legend.

axes

if set to "all" (default value) x axes are drawn for each plot in the graphic. If set to "bottom" and group is used, axes are drawn only under the plots located at the bottom of the graphic area. If FALSE, no x axis is drawn.

...

other parameters that will be passed to imagefunc or seqplot (for seqtree2dot).

Details

These functions generate a "dot" file that can be used in GraphViz (http://www.graphviz.org). It also generates one image per node through a call to imagefunc passing the selected lines of imagedata if present or otherwise a list of indexes (of individuals belonging to a node). These functions are not intended to be used by end-user. See seqtreedisplay and disstreedisplay for a much simpler way to generate a graphical representation of a tree (seqtree or disstree).

seqtree2dot is a shortcut for sequences objects using the plot function seqplot. For each node, it calls seqplot with the corresponding subset of rows of seqdata and the provided seqplot's arguments. You should at least specify the type of the plot (e.g. type="d", see seqplot for more details).

If use.title is TRUE, imagefunc should take care to leave enough space for the title.

disstree2dotp is a simplified interface of disstree2dot which automatically leaves enough space for the title and subtitles. These functions are intended to be generic.

Value

Nothing but generates a "dot" and several image files (one per node) in the current working directory (see getwd and setwd).

Author(s)

Matthias Studer (with Gilbert Ritschard for the help page)

See Also

seqtree and seqtreedisplay, disstree and disstreedisplay.

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