plotProfile {GLAD}R Documentation

Plot genomic profile and cytogenetic banding

Description

Plot genomic profile with breakpoints, outliers, smoothing line and cytogenetic banding.

Usage


plotProfile.profileCGH(profileCGH, variable="LogRatio", Chromosome=NULL,
                       Smoothing=NULL, Bkp=FALSE,
                       labels=TRUE, plotband=TRUE, unit=0,
                       colDAGLAD=c("black","blue","red","green","yellow"),
                       colCytoBand=c("white","darkblue"),
                       colCentro="red", text=NULL, ...)



Arguments

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.
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.
colCytoBand Color code for cytogenetic banding.
colCentro Color code for centromere.
text A list with the parameters to be passed to the function text.
...

Details

Value

A plot

Note

People interested in tools dealing with array CGH analysis can visit our web-page http://bioinfo.curie.fr.

Author(s)

Philippe Hupé, glad@curie.fr.

See Also

Examples


### 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")



[Package GLAD version 1.0.4 Index]