report.plot {MANOR} | R Documentation |
Displays an array image and a genomic representation of a normalized arrayCGH.
## 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, ...)
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 . |
This function successively calls arrayPlot
and genome.plot
.
People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.
Pierre Neuvial, manor@curie.fr.
genome.plot
, arrayPlot
, html.report
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))