plot.qb.scanone {qtlbim} | R Documentation

## Plot or print qb.scanone object.

### Description

Plot or print marginal diagnostics of effects from a qb.scanone object.

### Usage

    ## S3 method for class 'summary.qb.scanone':
    print(x, digits = 3, ...)
    ## S3 method for class 'qb.scanone':
    print(x, digits = 3, ...)
    ## S3 method for class 'qb.scanone':
    plot(x, chr, smooth = 3, scan, ylim,
      scan.name, col, main, sub, verbose = FALSE, ...)

### Arguments

`x` | An object of class `qb.scanone`.
`digits` | Significant digits to round with print.
`chr` | Vector of chromosomes to plot. Must be integer.
`smooth` | Perform smoothing if > 0 using weighted average over `smooth` adjacent points.
`scan` | The model effects to include, the default is all those included in the `scanone` object `x`.
`ylim` | Limits for vertical (y) axis; default uses data limits.
`scan.name` | Name used in automatically generated main title.
`col` | Named vector of colors for plot. Names of colors correspond to effects to be plotted. Unnamed colors will be made `"black"`.
`main` | Main title for the plot
`sub` | Subtitle for the plot; default is color names if not too long
`verbose` | Give verbose feedback if `TRUE`.
`...` | Other values passed to the generic plot function.

### Details

This plot method uses `plot.scanone` as the engine to plot marginal posterior diagnostics created with `qb.scanone`. When there are multiple effects in `x`, these may be organized into one or several stacked plots using `scan`. The default for most diagnostics except counts is `scan` = c("sum", "main", "epis"). Counts and posterior diagnostics are typically plotted in two stacked plots. Individual columns from the `x` object can be plotted by specifying their names as a vector to option `scan`.

### Value

Colors used in plots as character vector.

### Author(s)

Brian S. Yandell, yandell@stat.wisc.edu

### References

http://www.qtlbim.org

### See Also

`qb.scanone`, `summary.qb.scanone`, `plot.scanone`

### Examples

    example(qb.scanone)

[Package qtlbim version 1.6.5 Index]