trace.plot {RJaCGH} | R Documentation |
A trace plot with the trajectory of the Markov Chain.
trace.plot(x, k = NULL, array = NULL, Chrom = NULL, main.text = NULL)
x |
any of RJaCGH, RJaCGH.Chrom, RJaCGH.Genome, RJaCGH.array objects |
k |
Model to plot (i.e., number of hidden states). If NULL, the most visited is taken. |
array |
the name of the array to plot. |
Chrom |
the number of the chromosome to plot. |
main.text |
Main text of the plot |
This is simply a call to matplot
to show the values
sampled in the chain.
The colors does not correspond to any particular level of gain/loss.
A plot is drawn.
Oscar M. Rueda and Ramon Diaz
Rueda OM, Diaz-Uriarte R. Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH. PLoS Comput Biol. 2007;3(6):e122
RJaCGH
,
summary.RJaCGH
, modelAveraging
,
plot.RJaCGH
, states
,
y <- c(rnorm(100, 0, 1), rnorm(10, -3, 1), rnorm(20, 3, 1), rnorm(100, 0, 1)) Pos <- sample(x=1:500, size=230, replace=TRUE) Pos <- cumsum(Pos) Chrom <- rep(1:23, rep(10, 23)) jp <- list(sigma.tau.mu=rep(0.5, 5), sigma.tau.sigma.2=rep(0.3, 5), sigma.tau.beta=rep(0.7, 5), tau.split.mu=0.5, tau.split.beta=0.5) fit.genome <- RJaCGH(y=y, Pos=Pos, Chrom=Chrom, model="Genome", burnin=10, TOT=100, jump.parameters=jp, k.max = 5) trace.plot(fit.genome, array="array1")