disstree2dot: Graphical representation of a dissimilarity tree

In TraMineR: Trajectory Miner: a Sequence Analysis Toolkit

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)

See Also

seqtree and seqtreedisplay, disstree and disstreedisplay.

TraMineR documentation built on May 29, 2024, 5 a.m.