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$cloneValues
defining the color legend
clim
a numeric vector of length 2: color range limits (used if col.var is numeric)
cex
a numerical value giving the amount by which plotting text
and symbols should be scaled relative to the default: see par
xlab
a title for the x axis: see title
ylab
a title for the y axis: see title
pch
either an integer specifying a symbol or a single character
to be used as the default in plotting points: see par
...
further arguments to be passed to plot
Details
if col.var is a numeric variable, y colors are
proportionnal to col.var values; if it is a character variable
or a factor, one color is assigned to each different value of
col.var. If col.var is NULL, colors are proportionnal to
y values.
Note
People interested in tools for array-CGH analysis can
visit our web-page: http://bioinfo.curie.fr.
data(spatial)
## default color code: log-ratios
## Not run:
genome.plot(edge.norm, chrLim="LimitChr")
## End(Not run)
## color code determined by a qualitative variable: ZoneGNL (DNA copy number code)
edge.norm$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)
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(MANOR)
Loading required package: GLAD
######################################################################################
Have fun with GLAD
For smoothing it is possible to use either
the AWS algorithm (Polzehl and Spokoiny, 2002,
or the HaarSeg algorithm (Ben-Yaacov and Eldar, Bioinformatics, 2008,
If you use the package with AWS, please cite:
Hupe et al. (Bioinformatics, 2004, and Polzehl and Spokoiny (2002,
If you use the package with HaarSeg, please cite:
Hupe et al. (Bioinformatics, 2004, and (Ben-Yaacov and Eldar, Bioinformatics, 2008,
For fast computation it is recommanded to use
the daglad function with smoothfunc=haarseg
######################################################################################
New options are available in daglad: see help for details.
Attaching package: 'MANOR'
The following object is masked from 'package:base':
norm
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/MANOR/genome.plot.Rd_%03d_medium.png", width=480, height=480)
> ### Name: genome.plot
> ### Title: Pan-genomic representation of a normalized arrayCGH
> ### Aliases: genome.plot genome.plot.default genome.plot.arrayCGH
> ### Keywords: hplot
>
> ### ** Examples
>
> data(spatial)
>
> ## default color code: log-ratios
> ## Not run:
> ##D 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:
> ##D 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:
> ##D genome.plot(gradient.nonorm, pch=20, main="Genomic profile without
> ##D normalization", chrLim="LimitChr")
> ##D x11()
> ##D genome.plot(gradient.norm, pch=20, main="Genomic profile with
> ##D normalization", chrLim="LimitChr")
> ## End(Not run)
>
>
>
>
>
> dev.off()
null device
1
>