genome.plot: Pan-genomic representation of a normalized arrayCGH

In MANOR: CGH Micro-Array NORmalization

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, [e-mail].

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)

MANOR documentation built on Nov. 8, 2020, 6:52 p.m.