genome.plot {MANOR} | R Documentation |
Displays a pan-genomic representation of a normalized arrayCGH.
## 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="", ...)
arrayCGH |
an object of type arrayCGH |
data |
a data frame with two columns: 'x' and 'y', and optionally a column data$chrLim giving the limits of each chromosome |
x |
a variable name from arrayCGH\$cloneValues giving the order position
of the clones along the genome (defaults to 'PosOrder') |
y |
a variable name from arrayCGH\$cloneValues to be plotted along the
genome (defaults to 'LogRatio') |
chrLim |
an optional variable name from arrayCGH\$cloneValues
giving the limits of each chromosome |
col.var |
a variable name from arrayCGH\$cloneValues
defining the color legend |
clim |
a numeric vector of length 2: color range limits (used if col.var is numeric) |
cex |
a numerical value giving the amount by which plotting text
and symbols should be scaled relative to the default: see par |
xlab |
a title for the x axis: see title |
ylab |
a title for the y axis: see title |
pch |
either an integer specifying a symbol or a single character
to be used as the default in plotting points: see par |
... |
further arguments to be passed to plot |
if col.var
is a numeric variable, y
colors are
proportionnal to col.var
values; if it is a character variable
or a factor, one color is assigned to each different value of
col.var
. If col.var
is NULL, colors are proportionnal to
y
values.
People interested in tools for array-CGH analysis can visit our web-page: http://bioinfo.curie.fr.
Pierre Neuvial, manor@curie.fr.
data(spatial) ## default color code: log-ratios ## Not run: genome.plot(edge.norm, chrLim="LimitChr") ## End(Not run) ## color code determined by a qualitative variable: ZoneGNL (DNA copy number code) edge.norm$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.arrayCGH(gradient, flag.list=NULL, var="LogRatio", FUN=median, na.rm=TRUE) gradient.nonorm <- sort.arrayCGH(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)