report.plot {MANOR} | R Documentation

## Array image and a genomic representation of a normalized arrayCGH

### Description

Displays an array image and a genomic representation of a normalized arrayCGH.

### Usage

    ## S3 method for class 'arrayCGH':
    report.plot(arrayCGH, x="PosOrder", y=c("LogRatioNorm",
      "LogRatio"), chrLim=NULL, layout=TRUE, main=NULL, zlim=NULL, ...)
    ## Default S3 method:
    report.plot(spot.data, clone.data, design, x="PosOrder",
      y=c("LogRatioNorm", "LogRatio"), chrLim=NULL, layout=TRUE, main=NULL,
      zlim=NULL, ...)

### Arguments

`arrayCGH` | an object of type `arrayCGH`.
`spot.data` | data.frame with spot-level information to be passed to arrayPlot.
`clone.data` | data.frame with clone-level information to be passed to genome.plot.
`design` | vector of length 4 with array design: number of blocks per column and per row, number of columns and rows per block.
`x` | a variable name from arrayCGH$cloneValues giving the order position of the clones along the genome.
`y` | a vector of one or two variable names to be plotted on the array and along the genome. The first one is taken from `arrayCGH\$arrayValues` and is plotted on the array; the second one (or the first one if only one name was provided) is taken from `arrayCGH\$cloneValues` and is plotted along the genome.
`chrLim` | an optional variable name from arrayCGH$cloneValues giving the limits of each chromosome.
`layout` | if `TRUE`, plot layout is set to a 1*2 matrix with relative column widths 1 and 4.
`main` | title for the genomic profile.
`zlim` | numeric vector of length 2 to be passed to `arrayPlot`: minimum and maximum signal values for array image display.
`...` | further arguments to be passed to `genome.plot`.

### Details

This function successively calls `arrayPlot` and `genome.plot`.

### Note

People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.

### Author(s)

Pierre Neuvial, manor@curie.fr.

### See Also

`genome.plot`, `arrayPlot`, `html.report`

### Examples

    data(spatial)

    ### edge: local spatial bias
    ## aggregate arrayCGH without normalization for comparison with
    ## normalized array
    edge.nonorm <- norm.arrayCGH(edge, flag.list=NULL, FUN=median, na.rm=TRUE)
    edge.nonorm <- sort.arrayCGH(edge.nonorm, position.var="PosOrder")

    layout(matrix(c(1,2,4,5,3,3,6,6), 4,2),width=c(1, 4), height=c(6,1,6,1))
    report.plot(edge.nonorm, chrLim="LimitChr", layout=FALSE,
    main="Pangenomic representation (before normalization)", zlim=c(-1,1),
    ylim=c(-3,1))
    report.plot(edge.norm, chrLim="LimitChr", layout=FALSE,
    main="Pangenomic representation (after normalization)", zlim=c(-1,1),
    ylim=c(-3,1))

    ### gradient: global array Trend
    ## aggregate arrayCGH without normalization for comparison with
    ## normalized array
    gradient.nonorm <- norm.arrayCGH(gradient, flag.list=NULL, FUN=median, na.rm=TRUE)
    gradient.nonorm <- sort.arrayCGH(gradient.nonorm)

    layout(matrix(c(1,2,4,5,3,3,6,6), 4,2),width=c(1, 4), height=c(6,1,6,1))
    report.plot(gradient.nonorm, chrLim="LimitChr", layout=FALSE,
    main="Pangenomic representation (before normalization)", zlim=c(-2,2),
    ylim=c(-3,2))
    report.plot(gradient.norm, chrLim="LimitChr", layout=FALSE,
    main="Pangenomic representation (after normalization)", zlim=c(-2,2),
    ylim=c(-3,2))

[Package MANOR version 1.14.0 Index]