plot.scantwo {qtl} | R Documentation |

Plot the results of a two-dimensional, two-QTL genome scan.

plot.scantwo(x, chr, incl.markers=FALSE, zlim, lower=c("cond-int","cond-add","joint"), nodiag=TRUE, contours=FALSE, main, zscale=TRUE, col.scheme = c("redblue","cm","gray","heat","terrain","topo"), gamma=1, ...)

`x` |
An object of class `"scantwo"` , as output by
`scantwo` . |

`chr` |
Vector specifying which chromosomes to plot. |

`incl.markers` |
If FALSE, plot LOD scores on an evenly spaced grid (not including the results at the markers). |

`zlim` |
A vector of length 2 (optional), indicating the z limits for the joint LOD and the epistasis LOD scores, respectively. If missing, the maximum limits are used for each. |

`lower` |
Indicates which LOD scores should be plotted in the lower triangle. See the details below. |

`nodiag` |
If TRUE, suppress the plot of the scanone output (which is normally along the diagonal.) |

`contours` |
If TRUE, add a contour to the plot at 1.5-LOD below
its maximum, using a call to `contour` . If a
numeric vector, contours are drawn at these values below the maximum
LOD. |

`main` |
An optional title for the plot. |

`zscale` |
If TRUE, a color scale is plotted at the right. |

`col.scheme` |
Name of color pallet. |

`gamma` |
Parameter affecting range of colors when
`col.scheme="gray"` or `="redblue"` . |

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

Uses `image`

to plot a grid of LOD scores. The
upper triangle contains the epistasis LOD scores; the content in the
lower triangle depends on the input argument `lower`

.
The diagonal contains either all zeros or the main effects LOD scores
(from `scanone`

).

The `scantwo`

function calculates, for each pair of
putative QTLs, *(q1,q2)*, the likelihood undering the
null model *L0*, the likelihood under each of the single-QTL
models, *L(q1)* and *L(q2)*, the likelihood
under an additive QTL model, *La(q1,q2)*, and the
likelihood under a full QTL model (including QTL-QTL interaction),
*Lf(q1,q2)*.

The upper triangle in plot from this function contains the epistasis
LOD scores, *LODi = log10 Lf(q1,q2) - log10 Lf(q1,q2)*.

If `lower="joint"`

, the lower triangle will contain the joint LOD
scores, *LODi = log10 Lf(q1,q2) - log10 L0*.

If `lower="cond-int"`

, the lower triangle will contain LOD scores
comparing the two-QTL joint likelihood to the best of the single-QTL models,
*LODci = log10 Lf(q1,q2) - log10 max(L(q1), L(q2))*.

If `lower="cond-add"`

, the lower triangle will contain LOD scores
comparing the two-QTL additive likelihood to the best of the single-QTL models,
*LODca = log10 La(q1,q2) - log10 max(L(q1), L(q2))*.

If a color scale is plotted (`zscale=TRUE`

), the axis on the
left indicates the scale for the epistasis LOD scores (the upper
triangle), while the axis on the right indicates the scale for the
lower triangle. Note that the axis labels get screwed up
if you change the size of the figure window; you'll need to redo the
plot.

None.

Hao Wu, hao@jax.org; Karl W Broman, kbroman@jhsph.edu; Brian Yandell

`scantwo`

,
`summary.scantwo`

, `plot.scanone`

data(fake.f2) fake.f2 <- calc.genoprob(fake.f2, step=5) out.2dim <- scantwo(fake.f2, method="hk", chr=c(1,8,13,14)) plot(out.2dim) plot(out.2dim, nodiag=FALSE) plot(out.2dim, lower="joint", nodiag=FALSE)

[Package *qtl* version 0.98-57 Index]