genome.plot {MANOR} | R Documentation

## Pan-genomic representation of a normalized arrayCGH

### Description

Displays a pan-genomic representation of a normalized arrayCGH.

### Usage

      ## S3 method for class 'arrayCGH':
      genome.plot(arrayCGH, x="PosOrder", y="LogRatio",
        chrLim=NULL, col.var=NULL, clim=NULL, cex=NULL, pch=NULL, ...)
      ## Default S3 method:
      genome.plot(data, pch=NULL, cex=NULL, xlab="", ylab="", ...)

### Arguments

`arrayCGH` | an object of type `arrayCGH`
`data` | a data frame with two columns: 'x' and 'y', and optionally a column data$chrLim giving the limits of each chromosome
`x` | a variable name from `arrayCGH\$cloneValues` giving the order position of the clones along the genome (defaults to 'PosOrder')
`y` | a variable name from `arrayCGH\$cloneValues` to be plotted along the genome (defaults to 'LogRatio')
`chrLim` | an optional variable name from `arrayCGH\$cloneValues` giving the limits of each chromosome
`col.var` | a variable name from `arrayCGH\$cloneValues` defining the color legend
`clim` | a numeric vector of length 2: color range limits (used if `col.var` is numeric)
`cex` | a numerical value giving the amount by which plotting text and symbols should be scaled relative to the default: see `par`
`xlab` | a title for the x axis: see `title`
`ylab` | a title for the y axis: see `title`
`pch` | either an integer specifying a symbol or a single character to be used as the default in plotting points: see `par`
`...` | further arguments to be passed to `plot`

### Details

if `col.var` is a numeric variable, `y` colors are proportionnal to `col.var` values; if it is a character variable or a factor, one color is assigned to each different value of `col.var`. If `col.var` is NULL, colors are proportionnal to `y` values.

### 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

`flag`, `report.plot`

### Examples

    data(spatial)

    ## default color code: log-ratios
    ## Not run:
    genome.plot(edge.norm, chrLim="LimitChr")
    ## End(Not run)

    ## color code determined by a qualitative variable: ZoneGNL (DNA copy number code)
    edge.norm$cloneValues$ZoneGNL <- as.factor(edge.norm$cloneValues$ZoneGNL)
    ## Not run:
    genome.plot(edge.norm, col.var="ZoneGNL")
    ## End(Not run)
    ## comparing profiles with and without normalization
    ## aggregate data without normalization (flags)

    gradient.nonorm <- norm(gradient, flag.list=NULL, var="LogRatio",
    FUN=median, na.rm=TRUE)
    gradient.nonorm <- sort(gradient.nonorm)

    ## Not run:
    genome.plot(gradient.nonorm, pch=20, main="Genomic profile without
    normalization", chrLim="LimitChr")
    x11()
    genome.plot(gradient.norm, pch=20, main="Genomic profile with
    normalization", chrLim="LimitChr")
    ## End(Not run)

[Package MANOR version 1.16.0 Index]