genoClusterPlot {GWASTools} | R Documentation

## SNP cluster plots

### Description

Generates either X,Y or R,Theta cluster plots for specified SNP's.

### Usage

    genoClusterPlot(intenData, genoData, plot.type = c("RTheta", "XY"),
                    snpID, main.txt = NULL, by.sex = FALSE,
                    scan.sel = NULL, scan.hilite = NULL,
                    start.axis.at.0 = FALSE,
    		colors = c("default", "neon", "primary"),
                    verbose = TRUE, ...)

    genoClusterPlotByBatch(intenData, genoData, plot.type = c("RTheta", "XY"),
                           snpID, batchVar, main.txt = NULL, scan.sel = NULL,
                           colors = c("default", "neon", "primary"),
                           verbose = TRUE, ...)

### Arguments

`intenData` | `IntensityData` object containing 'X' and 'Y' values.
`genoData` | `GenotypeData` object
`plot.type` | The type of plots to generate. Possible values are "RTheta" (default) or "XY".
`snpID` | A numerical vector containing the SNP number for each plot.
`batchVar` | A character string indicating which annotation variable should be used as the batch.
`main.txt` | A character vector containing the title to give to each plot.
`by.sex` | Logical value specifying whether to indicate sex on the plot. If `TRUE`, sex must be present in intenData or genoData.
`scan.sel` | integer vector of scans to include in the plot. If `NULL`, all scans will be included.
`scan.hilite` | integer vector of scans to highlight in the plot with different colors. If `NULL`, all scans will be plotted with the same colors.
`start.axis.at.0` | Logical for whether the min value of each axis should be 0.
`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.
`verbose` | Logical value specifying whether to show progress.
`...` | Other parameters to be passed directly to `plot`.

### Details

Either 'RTheta' (default) or 'XY' plots can be generated. R and Theta values are computed from X and Y using the formulas `r <- x+y` and `theta <- atan(y/x)*(2/pi)`.

If `by.sex==TRUE`, females are indicated with circles and males with crosses.

### Author(s)

Caitlin McHugh

### See Also

`IntensityData`, `GenotypeData`

### Examples

    # create data object
    library(GWASdata)
    data(illuminaScanADF, illuminaSnpADF)

    xyfile <- system.file("extdata", "illumina_qxy.gds", package="GWASdata")
    xy <- GdsIntensityReader(xyfile)
    xyData <-  IntensityData(xy, scanAnnot=illuminaScanADF, snpAnnot=illuminaSnpADF)

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

    # select first 9 snps
    snpID <- illuminaSnpADF$snpID[1:9]
    rsID <- illuminaSnpADF$rsID[1:9]

    par(mfrow=c(3,3)) # plot 3x3
    genoClusterPlot(xyData, genoData, snpID=snpID, main.txt=rsID)

    # select samples
    scan.sel <- illuminaScanADF$scanID[illuminaScanADF$race == "CEU"]
    genoClusterPlot(xyData, genoData, snpID=snpID, main.txt=rsID,
                    scan.sel=scan.sel, by.sex=TRUE)

    genoClusterPlot(xyData, genoData, snpID=snpID, main.txt=rsID,
                    scan.hilite=scan.sel)
    close(xyData)
    close(genoData)

    ## affy data - cluster plots by plate
    data(affyScanADF, affySnpADF)

    xyfile <- system.file("extdata", "affy_qxy.nc", package="GWASdata")
    xy <- NcdfIntensityReader(xyfile)
    xyData <-  IntensityData(xy, scanAnnot=affyScanADF, snpAnnot=affySnpADF)

    genofile <- system.file("extdata", "affy_geno.nc", package="GWASdata")
    geno <- NcdfGenotypeReader(genofile)
    genoData <-  GenotypeData(geno, scanAnnot=affyScanADF, snpAnnot=affySnpADF)

    # select first 9 snps
    snpID <- affySnpADF$snpID[1:9]
    rsID <- affySnpADF$rsID[1:9]

    genoClusterPlotByBatch(xyData, genoData, snpID=snpID, main.txt=rsID,
                           batchVar="plate")
    close(xyData)
    close(genoData)

[Package GWASTools version 1.40.0 Index]