plot.rf {qtl} | R Documentation |

## Plot recombination fractions

### Description

Plot a grid showing the recombination fractions for all pairs of
markers, or of the LOD scores between pairs of markers.

### Usage

plot.rf(x, chr, which=c("both","lod","rf"), ...)

### Arguments

`x` |
An object of class `cross` . See
`read.cross` for details. |

`chr` |
Vector specifying which chromosomes to plot
(optional) |

`which` |
Indicate whether to plot LOD scores, recombination
fractions or both. |

`...` |
Ignored at this point. |

### Details

Uses `image`

to plot a grid showing the
recombination fractions and/or LOD scores for all pairs of markers.
(The LOD scores are for a test of *r = 1/2*.)
If both are plotted, the recombination fractions are in the upper left
triangle while the LOD scores are in the lower right triangle.
Red corresponds to a large LOD or a small recombination fraction,
while blue is the reverse. Note that missing values appear in light
gray.

Recombination fractions are transformed by *-4(log2(r)+1)* to make them on the same sort of scale as LOD
scores. Values of LOD or the transformed recombination fraction that
are above 12 are set to 12.

### Value

None.

### Author(s)

Karl W Broman, kbroman@jhsph.edu

### See Also

`est.rf`

, `image`

,
`badorder`

, `ripple`

### Examples

data(badorder)
badorder <- est.rf(badorder)
plot.rf(badorder)
# plot just chr 1
plot.rf(badorder,chr=1)
# plot just the recombination fractions
plot.rf(badorder,which="rf")
# plot just the LOD scores, and just for chr 2 and 3
plot.rf(badorder,which="lod")

[Package

*qtl* version 0.98-57

Index]