| plotProfile {GLAD} | R Documentation |
Plot genomic profile with breakpoints, outliers, smoothing line and cytogenetic banding.
## S3 method for class 'profileCGH':
plotProfile(profileCGH, variable="LogRatio", Chromosome=NULL,
Smoothing=NULL, GNL="ZoneGNL", Bkp=FALSE,
labels=TRUE, plotband=TRUE, unit=0,
colDAGLAD=c("black","blue","red","green","yellow"),
pchSymbol=c(20,13),
colCytoBand=c("white","darkblue"),
colCentro="red", text=NULL, main="", ylim=NULL, ...)
profileCGH |
Object of class profileCGH |
variable |
The variable to be plot. |
Chromosome |
A numeric vector with chromosome number to be
plotted. Use 23 and 24 for chromosome X and Y respectively. If
NULL, all the genome is plotted. |
Smoothing |
The variable used to plot the smoothing line. If
NULL, nothing is plotted. |
GNL |
The variable used to plot the Gain, Normal and Loss color code. |
Bkp |
If TRUE, the breakpoints are represented by a
vertical red dashed line. |
labels |
If TRUE, the labels of the cytogenetic banding
are written. |
plotband |
If TRUE, the cytogenetic banding are plotted. |
unit |
Give the unit of the PosBase. For example if unit=3,
PosBase are in Kb, if unit=6, PosBase are in Mb, ... |
colDAGLAD |
Color code to plot Deletion, Amplification, Gain, Lost and Normal status. |
pchSymbol |
A vector of two elements to specify the symbol tu be used for plotting point. pchSymbol[2] is the symbol for outliers. |
colCytoBand |
Color code for cytogenetic banding. |
colCentro |
Color code for centromere. |
text |
A list with the parameters to be passed to the function
text. |
main |
title of the plot. |
ylim |
range of the y-axis |
... |
" "
A plot
People interested in tools dealing with array CGH analysis can visit our web-page http://bioinfo.curie.fr.
Philippe Hupé, glad@curie.fr.
" "
### Cytogenetic banding information
data(cytoband)
###
data(snijders)
### Creation of "profileCGH" object
profileCGH <- as.profileCGH(gm13330)
###########################################################
###
### glad function as described in Hupé et al. (2004)
###
###########################################################
res <- glad(profileCGH, mediancenter=FALSE,
smoothfunc="lawsglad", bandwidth=10, round=2,
model="Gaussian", lkern="Exponential", qlambda=0.999,
base=FALSE,
lambdabreak=8, lambdacluster=8, lambdaclusterGen=40,
type="tricubic", param=c(d=6),
alpha=0.001, msize=5,
method="centroid", nmax=8,
verbose=FALSE)
### Genomic profile on the whole genome
plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, Smoothing="Smoothing", plotband=FALSE)
### Genomic profile on the whole genome and cytogenetic banding
plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, Smoothing="Smoothing")
### Genomic profile for chromosome 1
text <- list(x=c(90000,200000),y=c(0.15,0.3),labels=c("NORMAL","GAIN"), cex=2)
plotProfile(res, unit=3, Bkp=TRUE, labels=TRUE, Chromosome=1,
Smoothing="Smoothing", plotband=FALSE, text=text)
### Genomic profile for chromosome 1 and cytogenetic banding with labels
text <- list(x=c(90000,200000),y=c(0.15,0.3),labels=c("NORMAL","GAIN"), cex=2)
plotProfile(res, unit=3, Bkp=TRUE, labels=TRUE, Chromosome=1,
Smoothing="Smoothing", text=text, main="Chromosome 1")