seqtreedisplay: Graphical rendering of a sequence regression tree

Description

Generate a graphical representation of a regression tree of state sequence data.

Usage

seqtreedisplay(tree, filename = NULL, seqdata = tree$info$object,
  only.leaf = FALSE, sortv = NULL, diss = NULL, cex.main = 3,
  with.legend = "auto", cex.legend = cex.main, xaxis = FALSE,
  image.format = "png", with.quality = TRUE, cex.quality = cex.main,
  legend.text = NULL, show.tree = TRUE, show.depth = FALSE,
  imgLeafOnly, dist.matrix, title.cex, withlegend, legend.fontsize,
  imageformat, withquality, quality.fontsize, legendtext, showtree,
  showdepth, axes, ...)
disstreedisplay(tree, filename = NULL, image.data= NULL, image.fun = plot,
  only.leaf = FALSE, cex.main = 3, image.format = "png",
  with.quality = TRUE, cex.quality = cex.main,
  legend.text = NULL, show.tree = TRUE, show.depth = FALSE,
  imagedata, imagefunc, imgLeafOnly, title.cex, imageformat,
  withquality, quality.fontsize, legendtext, showtree, showdepth, ...)

Value

None

Arguments

tree: A seqtree object (as produced by seqtree) for seqtreedisplay. A disstree object (as produced by disstree) for disstreedisplay.
filename: The name of a file where to save the plot (overwritting existing file). If NULL, a temporary file is created.
seqdata: The sequence object containing the state sequences plotted in the nodes.
only.leaf: Logical. If TRUE sequences are plotted only in terminal nodes.
sortv: Argument passed to seqplot
diss: Argument passed to seqplot
cex.main: Node title magnification. See par.
with.legend: Logical. Should the color legend be displayed on the plot?
cex.legend: Legend magnification. See par. If not specified, use the value of cex.main.
xaxis: Logical. Should the x-axis be displayed on the plots? (argument passed to seqplot)
image.format: Image format of the output file (filename)
with.quality: If TRUE, a node displaying fitting measures of the tree is added to the plot.
cex.quality: Fitting measure text magnification. See par. If not specified, use the value of cex.main.
legend.text: Character. Optional text information that should be added.
show.tree: Logical. Should the tree be shown on the screen?
show.depth: Logical. If TRUE, the splits are ordered according to their global pseudo-R2.
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.
imgLeafOnly: Deprecated. Use only.leaf instead.
dist.matrix: Deprecated. Use diss instead.
title.cex: Deprecated. Use cex.main instead.
withlegend: Deprecated. Use with.legend instead.
legend.fontsize: Deprecated. Use cex.legend instead.
imageformat: Deprecated. Use image.format instead.
withquality: Deprecated. Use with.quality instead.
quality.fontsize: Deprecated. Use cex.quality instead.
legendtext: Deprecated. Use legend.text instead.
showtree: Deprecated. Use show.tree instead.
showdepth: Deprecated. Use show.depth instead.
imagedata: Deprecated. Use image.data instead.
imagefunc: Deprecated. Use image.fun instead.
axes: Deprecated. Use xaxis instead.
...: additional arguments passed to seqplot

Author

Matthias Studer (with Gilbert Ritschard for the help page)

Details

This function generates a tree image. For each node, it invokes seqplot for the selected lines of seqdata as argument. You should at least specify the type of the plot to use (type="d" for instance, see seqplot for more details).

The plot is actually not generated as an R plot, but with GraphViz (www.graphviz.org). Hence, seqtreedisplay only works when GraphViz is correctly installed. If the path to GraphViz is not found, pass the path as a gvpath argument among the ... list.