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, axes = FALSE,
      imgLeafOnly, dist.matrix, title.cex,
      withlegend, withquality,  ...)

### 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.
`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.
`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.
`...` | 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`).

`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`.

[Package TraMineR version 2.2-2 Index]