MANOR (version 1.44.0)

report.plot: Array image and a genomic representation of a normalized arrayCGH

Description

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

Usage

"report.plot"(arrayCGH, x="PosOrder", y=c("LogRatioNorm", "LogRatio"), chrLim=NULL, layout=TRUE, main=NULL, zlim=NULL, ...)
"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.

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(edge, flag.list=NULL, FUN=median, na.rm=TRUE) 
edge.nonorm <- sort(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(gradient, flag.list=NULL, FUN=median, na.rm=TRUE) 
gradient.nonorm <- sort(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))