plot-PSTr: Plot a PST
In PST: Probabilistic Suffix Trees and Variable Length Markov Chains

Description Usage Arguments Details Author(s) References Examples

Plot a PST

	## S4 method for signature 'PSTf,ANY'
plot(x, y=missing, max.level=NULL,
		nodePar = list(), edgePar = list(),
		axis=FALSE, xlab = NA, ylab = if (axis) { "L" } else {NA}, 
		horiz = FALSE, xlim, ylim, 
		withlegend=TRUE, ltext=NULL, cex.legend=1, 
		use.layout=withlegend!=FALSE, legend.prop=NA, ...)

`x`	A PST, that is an object of class `PSTf` as returned by the `pstree` or `prune` method.
`y`	not applicable
`max.level`	integer. The maximal depth for the display of the tree.
`nodePar`	list. A list of parameters for tuning the node representation. Possible parameters are node.size. numeric. The size of the node, in fraction of a unit of the x axis (or y axis if horiz=TRUE). gratio. The ratio between horizontal and vertical dimensions of the node. usefull if the horizontal and vertical dimensions of the plot are not equal. If not provided, it is estimated as a function of the number of leaves represented in the plot and the depth of the tree.
`edgePar`	list. A list of parameters for tuning the edges representation. Possible paramters are
`axis`	logical. If TRUE the axes are displayed on the plot.
`xlab`	character. Label for the x axis.
`ylab`	character. Label for the y axis representing the tree depth.
`horiz`	logical. If FALSE, the tree is represented vertically. The root node at depth L=0 is plotted on the top, and the nodes of maximal depth are plotted on the bottom of the plot. If TRUE, the tree is represented horizontally. The root node at depth L=0 is plotted on the right, and the nodes of maximal depth are plotted on the left of the plot.
`xlim`	numeric. Vector of length 2 giving the x limits for the plot. By default the limits are 1 .. number of terminal nodes (at max.level if specified). This may be usefull to facilitate comparison if several trees are plotted on the same figure.
`ylim`	numeric. Vector of length 2 giving the y limits for the plot. By default the limits are 0 .. max. depth of the tree (max.level if specified). This may be usefull to facilitate comparison if several trees are plotted on the same figure.
`withlegend`	defines if and where the legend of the state colors is plotted. The default value `TRUE` sets the position of the legend automatically. Other possible value is `"right"`.
`ltext`	optional description of the states to appear in the legend. Must be a vector of character strings with number of elements equal to the size of the alphabet. If unspecified, the `label` attribute of the `seqdata` sequence object is used (see `seqdef`).
`cex.legend`	expansion factor for setting the size of the font for the labels in the legend. The default value is 1. Values lesser than 1 will reduce the size of the font, values greater than 1 will increase the size.
`use.layout`	if `TRUE`, `layout` is used to arrange plots when using the group option or plotting a legend. When layout is activated, the standard '`par(mfrow=....)`' for arranging plots does not work. With `withlegend=FALSE` and `group=NULL`, layout is automatically deactivated and '`par(mfrow=....)`' can be used.
`legend.prop`	sets the proportion of the graphic area used for plotting the legend when `use.layout=TRUE` and `withlegend=TRUE`. Default value is set according to the place (bottom or right of the graphic area) where the legend is plotted. Values from 0 to 1.
`...`	arguments to be passed to the plot function or graphical parameters

The function for graphical representation of a PST uses is recursive. The main argument of the function is a tree represented as a nested list (an object of class PSTr). See also Gabadinho 2016.

Alexis Gabadinho, based on code from plot.dendrogram

Gabadinho, A. & Ritschard, G. (2016). Analyzing State Sequences with Probabilistic Suffix Trees: The PST R Package. Journal of Statistical Software, 72(3), pp. 1-39.

data(s1)
s1 <- seqdef(s1)
S1 <- pstree(s1, L=3)
plot(S1)
plot(S1, horiz=TRUE)
plot(S1, nodePar=list(node.type="path", lab.type="prob", lab.pos=1, lab.offset=2, lab.cex=0.7), 
	edgePar=list(type="triangle"), withlegend=FALSE)

Loading required package: TraMineR

TraMineR stable version 2.0-7 (Built: "Sat,)
Website: http://traminer.unige.ch
Please type 'citation("TraMineR")' for citation information.

Loading required package: RColorBrewer

PST version 0.94 (Built: 2017-09-22)
Website: http://r-forge.r-project.org/projects/pst
 [>] 2 distinct states appear in the data: 
     1 = a
     2 = b
 [>] state coding:
       [alphabet]  [label]  [long label] 
     1  a           a        a
     2  b           b        b
 [>] 1 sequences in the data set
 [>] min/max sequence length: 27/27
 [>] 1 sequence(s) - min/max length: 27/27
 [>] max. depth L=3, nmin=1
     [L]  [nodes]
       0        1
       1        2
       2        4
       3        8
 [>] computing sequence(s) likelihood ... (0.01 secs)
 [>] total time: 0.291 secs
 [>] building 'PSTr' representation, max. depth=3... (0.014 secs)
There were 15 warnings (use warnings() to see them)
 [>] building 'PSTr' representation, max. depth=3... (0.003 secs)
There were 15 warnings (use warnings() to see them)
 [>] building 'PSTr' representation, max. depth=3... (0.001 secs)