plot.Rcpp_Trace {AnaCoDa}

Plot Trace Object

Description

Plots different traces, specified with the what parameter.

Usage

## S3 method for class 'Rcpp_Trace'
plot(
  x,
  what = c("Mutation", "Selection", "MixtureProbability", "Sphi", "Mphi", "Aphi",
    "Sepsilon", "ExpectedPhi", "Expression", "NSEProb", "NSERate", "InitiationCost",
    "PartitionFunction"),
  geneIndex = 1,
  mixture = 1,
  log.10.scale = F,
  ...
)

Arguments

x

An Rcpp trace object initialized with initializeTraceObject.

what

A string containing one of the following to graph: Mutation, Selection, Alpha, LambdaPrime, MeanWaitingTime, VarWaitingTime MixtureProbability, Sphi, Mphi, Aphi, Spesilon, ExpectedPhi, Expression.

geneIndex

When plotting expression, the index of the gene to be plotted.

mixture

The mixture for which to plot values.

log.10.scale

A logical value determining if figures should be plotted on the log.10.scale (default=F). Should not be applied to mutation and selection parameters estimated by ROC/FONSE.

...

Optional, additional arguments. For this function, may be a logical value determining if the trace is ROC-based or not.

Value

This function has no return value.