chromIntensityPlot {GWASTools} | R Documentation

## Plot B Allele Frequency and/or Log R Ratio, R or Theta values for samples by probe position on a chromosome

### Description

This function creates plots for one or more of the 'B AlleleFreq', 'Log R Ratio', 'R' or 'Theta' values for given sample by chromosome combinations.

### Usage

    chromIntensityPlot(intenData, scan.ids, chrom.ids,
      type = c("BAF/LRR", "BAF", "LRR", "R", "Theta", "R/Theta"),
      main = NULL, info = NULL, abln = NULL,
      horizln = c(1/2, 1/3, 2/3),
      colorGenotypes = FALSE, genoData = NULL,
      colorBatch = FALSE, batch.column = NULL,
      snp.exclude = NULL,
      ideogram=TRUE, ideo.zoom=TRUE, ideo.rect=FALSE,
      cex=0.5, cex.leg=1.5,
      colors = c("default", "neon", "primary"), ...)

### Arguments

`intenData` | `IntensityData` object, must contain at least one of 'BAlleleFreq', 'LogRRatio', 'X', 'Y'.
`scan.ids` | A vector containing the scan IDs to plot.
`chrom.ids` | A vector containing the chromosomes to plot for each scanID (should have same length as `scan.ids`).
`type` | The type of plot to be created. 'BAF/LRR' creates both 'B Allele Freq' and 'Log R Ratio' plots. 'R/Theta' creates both 'R' and 'Theta' plots.
`main` | Vector of plot titles. If `NULL` then the title will include scanID, sex, and chromosome.
`info` | A character vector containing extra information to include in the main title.
`abln` | A vector of values that is of length `2*length(scan.ids)`. Each pair of entries specifies where vertical lines will be drawn in each plot. This is especially useful when drawing the start \& end breakpoints for anomalies, for example. Use -1 as one pair value for plots that warrant only one line. By default, no lines will be drawn.
`horizln` | A vector containing the y-axis values at which a horizontal line will be drawn in B Allele Frequency plots.
`colorGenotypes` | A logical value specifying whether to color-code the points by called genotype. if `TRUE`, genoData must be given also.
`genoData` | `GenotypeData` object, required if colorGenotypes=`TRUE`.
`colorBatch` | A logical value specifying whether to color-code the points by sample batch (e.g, plate). If `TRUE`, batch.column must also be specified.
`batch.column` | A character string indicating which annotation variable in intenData should be used as the batch.
`snp.exclude` | An integer vector giving the IDs of SNPs to exclude from the plot.
`ideogram` | logical for whether to plot a chromosome ideogram under the BAF and LRR plots.
`ideo.zoom` | logical for whether to zoom in on the ideogram to match the range of the BAF/LRR plots.
`ideo.rect` | logical for whether to draw a rectangle on the ideogram indicating the range of the BAF/LRR plots.
`cex` | cex value for points on the plots.
`cex.leg` | cex value for the ideogram legend.
`colors` | Color scheme to use for genotypes. "default" is colorblind safe (colorbrewer Set2), "neon" is bright orange/green/fuschia, and "primary" is red/green/blue.
`...` | Other parameters to be passed directly to `plot`.

### Details

For all plots, a vertical line is drawn every one eigth of the chromosome. For the Log R Ratio plot, the y-axis has been given the range of (-2,2).

### Author(s)

Caitlin McHugh, Cathy Laurie

### See Also

`IntensityData`, `GenotypeData`, `BAFfromGenotypes`

### Examples

    library(GWASdata)
    data(illuminaScanADF)

    blfile <- system.file("extdata", "illumina_bl.gds", package="GWASdata")
    bl <- GdsIntensityReader(blfile)
    intenData <-  IntensityData(bl, scanAnnot=illuminaScanADF)

    genofile <- system.file("extdata", "illumina_geno.gds", package="GWASdata")
    geno <- GdsGenotypeReader(genofile)
    genoData <-  GenotypeData(geno, scanAnnot=illuminaScanADF)

    scanID <- getScanID(illuminaScanADF, index=1)
    chromIntensityPlot(intenData=intenData, scan.ids=scanID,
                       chrom.ids=22, type="BAF/LRR", info="interesting sample",
                       colorGenotypes=TRUE, genoData=genoData)
    close(genoData)
    close(intenData)

[Package GWASTools version 1.40.0 Index]