plot.pREC_S {RJaCGH} | R Documentation

## Plot number of probes shared by pairs of arrays

### Description

An image plot showing the results of `pREC_S` on a group of arrays.

### Usage

    ## S3 method for class 'pREC_S'
    plot(x, array.labels = NULL,  stats = TRUE, col = NULL,
                          breaks = NULL, dend = TRUE, method = "single",
                          Chrom = NULL, ...)

### Arguments

`x` | An object of class `pREC_S`
`array.labels` | A vector for alternative labels for the arrays.
`Chrom` | Chromosome to plot. If `NULL`, all chromosomes are plotted.
`stats` | Logical. If `TRUE`, over every cell the number of common probes and the mean length is printed.
`col` | A vector of color codes for the image plot.
`breaks` | Breakpoints for the code color. Must be a vector of length length(col) + 1
`dend` | Logical. If `TRUE`, a clustering of arrays is performed with `hclust` and arrays reordered.
`method` | Clustering method to apply. See `hclust`. Default is 'single'.
`...` | Additional arguments passed to `image`

### Details

First, the number of probes shared by every pair of arrays and their mean length is computed. The plot consists of a square with as many rows and as many columns as the number of arrays are. The more altered probes two arrays share the brighter the color is. The diagonals are turned off to improve the visibility of the groups. If `dend` is `TRUE`, a hierarchical clustering (method `method`) on arrays is performed based on the dissimilarity measure defined as: $1 - (inc.mat / max(inc.mat))$ where `inc.mat` is the matrix with the number of arrays shared by every pair of arrays. Then a dendrogram is plotted and the arrays are reordered. The diagonals of the plot are turned off to improve the perception of the relationships between arrays. Note that the number of probes shared depends on the parameters passed to `pREC_S`, such as the probability threshold `p` and the minimum number of arrays requiered to form a region `freq.array`.

### Value

A list with elements

`probes` | Matrix with the number of probes shared by every pair of arrays.
`length` | Matrix with the mean length of probe shared by every pair of arrays.

### Author(s)

Oscar M. Rueda and Ramon Diaz Uriarte

### References

Rueda OM, Diaz-Uriarte R. Flexible and Accurate Detection of Genomic Copy-Number Changes from aCGH. PLoS Comput Biol. 2007;3(6):e122

### See Also

`pREC_S`, `hclust`, `image`

### Examples

    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(0.05, 4), sigma.tau.sigma.2=rep(0.03, 4),
               sigma.tau.beta=rep(0.07, 4), tau.split.mu=0.1, tau.split.beta=0.1)

    z <- c(rnorm(110, 0, 1), rnorm(20, 3, 1),
           rnorm(100,0, 1))
    zz <- c(rnorm(90, 0, 1), rnorm(40, 3, 1),
           rnorm(100,0, 1))

    fit.array.genome <- RJaCGH(y=cbind(y,z,zz),
    Pos=Pos, Chrom=Chrom, model="Genome",
    burnin=1000, TOT=1000, jump.parameters=jp, k.max = 4)
    Reg1 <- pREC_S(fit.array.genome, p=0.4, freq.array=2,
    alteration="Gain")
    plot(Reg1)

[Package RJaCGH version 2.0.4 Index]