R: Graphical representation of a dissimilarity tree

disstree2dot {TraMineR}

R Documentation

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,  ...)

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`).

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.

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)