# R/cplot.R In PST: Probabilistic Suffix Trees and Variable Length Markov Chains

```## Probability distribution of a node

setMethod("cplot", signature="PSTf",
def=function(object, context, state, main=NULL, all=FALSE, x.by=1, y.by=0.2, by.state=FALSE, ...) {

A <- object@alphabet
cpal <- c(object@cpal)
oolist <- list(...)

if (!missing(state) && is.character(state)) {
state <- which(state==A)
}

node <- query(object, context, output="all")
prob <- node@prob
pruned <- node@pruned

if (all) {
seglist <- object[[1]][[1]]@index
} else {
seglist <- node@index
}

if (is.null(main)) {
main <- paste("Node ", node@path)
}

plot(NULL, axes=FALSE, ylab="Prob", xlim=c(1,(nrow(seglist)+1)), ylim=c(1,0), main=main, ...)

## prob matrix is reversed because we are using the function for plotting the tree nodes (yaxis is reversed)
plotNodeProb(1, 1, nrow(seglist)+1, 0, prob=prob, seglist=seglist, cpal=cpal, pruned=pruned,
by.state=by.state, index=node@index)

if (length(seglist)>1) {
slab.pos <- seq(1, nrow(seglist), by=x.by)
axis(1, at=slab.pos+0.5, labels=seglist[slab.pos])
}
axis(2, at=seq(0,1, by=y.by), labels=rev(seq(0,1, by=y.by)))
}
)
```

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PST documentation built on May 2, 2019, 5:14 p.m.