plotSnp {SNPchip} | R Documentation

## Plots copy number and genotype calls.

### Description

Plots copy number and genotype call versus physical position for an arbitrary number of samples and chromosomes.

### Usage

    plotSnp(object, chromosomes, samples, snpId = c(NA, 1e+06), oma = c(5, 4, 4, 0.5), mar = c(0.5, 0, 0.5, 0.2), width.right = NULL, showLayout = FALSE, plot = TRUE, col = c("royalblue", "red", "royalblue", "green3"), bg = rep("white", 4), cex = c(2, 3, 2, 2), pch = rep(".", 4), col.centromere = c("bisque", NA), bw = FALSE, lwd = 2, col.axis = "brown", cex.axis = 1, cex.main = 1, cex.lab = 1, xlim = NULL, ylim = NULL, log = "", xaxis.side = rep(c(1, 3), length.out = length(chromosomes)), xaxs = "i", xaxt = "n", yaxs = "i", yaxt = "n", xlab = "", ylab = "", lab = c(2, 5, 7), adj = 0, main = "", legend = c(TRUE, TRUE), legend.panel = c(TRUE, FALSE), legend.location = c("topright", "bottomright"), legend.bty = c("n", "n"), legend.col = c("white", "white"), ncol = 2, cex.legend = c(1, 1), digits = 3, pt.cex = cex.legend * 1.5, bty = "n", addCytoband = FALSE, height.cytoband = 0.5, ...)

### Arguments

`object` | Object of class `AnnotatedSnpCopyNumberSet` or `AnnotatedSnpSet`
`chromosomes` | Vector of character strings for chromosome number. Chromosomes will be plotted in the order given.
`samples` | Vector of integers indicating sample number.
`snpId` | Not yet implemented.
`oma` | See `par`
`mar` | See `par`
`width.right` | Width of panel for the legend relative to the width of the smallest chromosome.
`showLayout` | Logical for whether to display the output of `layout` for plotting
`plot` | Logical. If FALSE, only the output from `layout` is displayed.
`col` | A character or numerical vector indicating the color to plot genotype call: AA color, AB color, BB color, no call color. For `AnnotatedSnpCopyNumberSet`, only the first color is used.
`bg` | A character or numerical vector indicating the background color for the plotting symbols. Possible to specify a different background for each genotype call in the same order as `col`.
`cex` | A numerical vector of plotting symbol size in the same order as `col`.
`pch` | A character or numerical vector of plotting symbol size in the same order as `col`.
`col.centromere` | Vector of length two: color of centromere and color for the centromere border.
`bw` | Converts all colors to grayscale.
`lwd` | See `par`
`col.axis` | See `par`
`cex.axis` | See `par`
`cex.main` | See `par`
`cex.lab` | See `par`
`xlim` | See `par`
`ylim` | See `par`
`log` | See `par`
`xaxis.side` | Vector of integers indicating whether to plot the x-axis on the top (3) or bottom (1) for each sample. The default is to alternate top/bottom.
`xaxs` | See `par`
`xaxt` | See `par`
`yaxs` | See `par`
`yaxt` | See `par`
`xlab` | See `par`
`ylab` | See `par`
`lab` | See `par`
`adj` | See `par`
`main` | See `par`
`legend` | Logical vector of length 2. If both are TRUE, a legend for descriptive statistics (legend 1) and plotting symbols (legend 2) are generated.
`legend.panel` | Logical vector of length 2. Whether to draw the legends on a separate panel.
`legend.location` | Character vector of length 2. Where to draw the legends. See `legend`.
`legend.bty` | Character vector of length 2. See the argument `bty` in function `legend`.
`legend.col` | Character vector of length 2. See the argument `bty` in function `legend`.
`ncol` | Number of columns in legend for plotting symbols. See `legend`.
`cex.legend` | Same as argument `cex` in function `legend`.
`digits` | Rounds values in legend to the number of digits specified.
`pt.cex` | See `legend`
`bty` | See `par`
`addCytoband` | Logical indicating whether to add a cytoband.
`height.cytoband` | Height of cytoband relative to height of samples.
`...` | Additional arguments

### Details

### Value

### Note

### Author(s)

Robert Scharpf

### References

### See Also

`par`, `plot`, `legend`

### Examples

    data(annSnpset)
    plotSnp(annSnpset, chromosomes=c(1:22, "X"),
            samples=1:4, width.right=10, cex.axis=1, lab=c(3, 3, 5),
            cex.lab=1.2, cex.legend=c(1, 1.2))

[Package SNPchip version 1.0.0 Index]