disstree2dot: Graphical representation of a dissimilarity tree

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

disstree2dot(tree, filename, digits = 3, image.fun = NULL, image.data = NULL,
  only.leaf = FALSE, device = "jpeg", image.format = "jpg",
  device.args = list(), use.title = TRUE, label.pos = "main",
  node.pos = "main", split.pos = "sub", cex.main = 1,
  legend.text = NULL, image.legend = NULL, image.quality = NULL,
  show.depth = FALSE, title.outer = FALSE,
  imagefunc, imagedata, imgLeafOnly, devicefunc, imageext,
  device.arg, label.loc, node.loc, split.loc, title.cex, legendtext,
  legendimage, qualityimage, showdepth, ...)
disstree2dotp(tree, filename, image.data = NULL, only.leaf = FALSE,
  image.fun = plot, cex.main = 3, with.quality = TRUE,
  cex.quality = cex.main, title.outer = FALSE,
  imagedata, imgLeafOnly, imagefunc, title.cex, withquality,
  quality.fontsize, ...)
seqtree2dot(tree, filename, seqdata = tree$info$object, only.leaf = FALSE,
  sortv = NULL, diss = NULL, cex.main = 3, with.legend = "auto",
  cex.legend = cex.main, with.quality = FALSE,
  cex.quality = cex.main, xaxis = FALSE,
  imgLeafOnly, dist.matrix, title.cex,
  withlegend, withquality, axes,  ...)

Value

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

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.
image.fun: A function to plot the individuals in a node, see details.
image.data: a data.frame that will be passed to image.fun, see details.
only.leaf: Logical: If TRUE, only terminal node will be plotted.
device: A device function, "jpeg" by default.
image.format: extension for image files.
device.args: Argument passed to device.
use.title: Logical: If TRUE, node information will be printed using title command, see details.
label.pos: Location of the node label, see title for possible values.
node.pos: Node content location, see title for possible values.
split.pos: Split information location, see title for possible values.
cex.main: 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.
legend.text: An optional text appearing in a distinct node.
image.legend: An optional image file appearing in a distinct node.
image.quality: An optional image file appearing in a distinct node.
show.depth: Logical. If TRUE, information about depth of the tree is added to the plot.
with.quality: If TRUE, a node displaying fitting measures of the tree is added to the plot.
cex.quality: 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.
diss: The name of an optional dissimilarity matrix used to find representative sequences, seqrplot.
with.legend: 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".
cex.legend: Size of the font of the legend.
xaxis: Logical. Should the x-axis be drawn on the plots?
imagefunc: Deprecated. Use image.fun instead.
imagedata: Deprecated. Use image.data instead.
imgLeafOnly: Deprecated. Use only.leaf instead.
devicefunc: Deprecated. Use device instead.
imageext: Deprecated. Use image.format instead.
device.arg: Deprecated. Use device.args instead.
label.loc: Deprecated. Use label.pos instead.
node.loc: Deprecated. Use node.pos instead.
split.loc: Deprecated. Use split.pos instead.
title.cex: Deprecated. Use cex.main instead.
legendtext: Deprecated. Use legend.text instead.
legendimage: Deprecated. Use image.legend instead.
qualityimage: Deprecated. Use image.quality instead.
showdepth: Deprecated. Use show.depth instead.
withquality: Deprecated. Use with.quality instead.
quality.fontsize: Deprecated. Use cex.quality instead.
dist.matrix: Deprecated. Use diss instead.
withlegend: Deprecated. Use with.legend instead.
axes: Deprecated. Use xaxis instead.
...: other parameters that will be passed to image.fun or seqplot (for seqtree2dot).

Author

Matthias Studer (with Gilbert Ritschard for the help page)

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 image.fun passing the selected lines of image.data 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).

If the path to GraphViz is not found, pass the path as gvpath argument among the ... list.

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, image.fun should take care to leave enough space for the title.