MANOR (version 1.44.0)

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

Description

Displays a pan-genomic representation of a normalized arrayCGH.

Usage

"genome.plot"(arrayCGH, x="PosOrder", y="LogRatio", chrLim=NULL, col.var=NULL, clim=NULL, cex=NULL, pch=NULL, ...)   "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.

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)