plot.bim.loci {bim} | R Documentation |

## Jittered plot of Bayesian QTL loci samples by chromosome

### Description

Each point is one locus from the Bayesian QTL estimates, plotted
vertically by chromosome, jittered to give a sense of density.

### Usage

plot.bim.loci(x, cross, nqtl=1, pattern=NULL, exact=FALSE,
chr, labels=TRUE, amount=.35, cex, ... )

### Arguments

`x` |
object of class `bim` |

`cross` |
corresponding object of class `cross` (extracted by
`bim.cross` if not provided) |

`nqtl` |
subset on number of QTL |

`pattern` |
subset on chromosome pattern of QTL |

`exact` |
subset on exact pattern or number of QTL if true |

`chr` |
subset of chromosomes to plot (numerical indices or chromosome names) |

`labels` |
include marker labels if TRUE |

`amount` |
amount of jitter (between 0 and .45) |

`cex` |
character expansion (may be invisible if too
small–default set by `bim.cex` ) |

`...` |
graphical parameters can be given as arguments to
`plot` |

### Details

Focuses attention on chromosome lengths and concentration of QTL loci
estimates. Horizontal blue lines at markers if `cross`

included. Adjust `amount`

and `cex`

to modify look of
plot. Most useful when looking at multiple chromosomes.

### Author(s)

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

### References

http://www.stat.wisc.edu/~yandell/qtl/software/Bmapqtl

### See Also

`jitter`

,`subset.bim`

### Examples

data( vern )
data( verngeo.bim )
plot.bim.loci( verngeo.bim, vern, 2 )

[Package

*bim* version 1.01-1

Index]