plotProfile {GLAD} | R Documentation

## Plot genomic profile and cytogenetic banding

### Description

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

### Usage

    ## 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, ...)

### 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.
`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
`...` | ...

### 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 HupÃ©, glad@curie.fr.

### See Also

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### Examples

    ### 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)

[Package GLAD version 2.46.0 Index]