plotProfile: Plot genomic profile and cytogenetic banding
In GLAD: Gain and Loss Analysis of DNA

Description Usage Arguments Details Value Note Author(s) See Also Examples

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,
                       cytoband = 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`.
`cytoband`	cytodand data. For human, cytoband data are avaibale using data(cytoband).
`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 HupÃ©, glad@curie.fr.

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### Cytogenetic banding information
data(cytoband)

###
data(snijders)

### Creation of "profileCGH" object
profileCGH <- as.profileCGH(gm13330)



###########################################################
###
###  glad function as described in HupÃ© 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)

### cytoband data to plot chromosome
data(cytoband)

### Genomic profile on the whole genome
plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE,
            Smoothing="Smoothing", plotband=FALSE, cytoband = cytoband)


### Genomic profile on the whole genome and cytogenetic banding
plotProfile(res, unit=3, Bkp=TRUE, labels=FALSE, Smoothing="Smoothing",
            cytoband = cytoband)


### 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, cytoband = cytoband)

### 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", cytoband = cytoband)