Description Usage Arguments Details Value Author(s) See Also Examples

View source: R/plot.locus.dist.R

Plots a phylogeny lined up with the locus-sharing similarity matrix in graphical style

1 2 3 4 5 |

`x` |
output from |

`tr` |
an object of class |

`trW` |
width of the panels holding the tree |

`plotW` |
width of the panel holding the matrix plot |

`labelsW` |
width of the panel holding the taxon labels (right side of plot) |

`plotGap` |
gap between the side panels and the central panel |

`scalar` |
the scalar for the dots in the locus distance plot |

`barH` |
height of the panel holding the bars |

`barW` |
width of individual bars; goes to |

`bar.cex` |
font size for numbers above the bars |

`point.pch` |
plot character ( |

`cols` |
color for the off-diagonal and diagonal elements of the matrix plot |

`...` |
additional arguments passed along to |

Use default options in `locus.dist`

to get a sensible plot.
Also, while different plotting characters can be defined for the off-diagonal and diagonal
elements of the matrix plot, these may be hard to compare with each other in size; probably
the diagonal elements are better distinguished by color or shading.

Currently, this function is implemented using `layout`

, which makes it rather clunky
and inflexible.

A list comprising:

`Xs` |
the x-coordinates of dots in the matrix plot |

`heights` |
heights of the bars at the top of the plot, which show the overlap of each individual averaged over all other individuals on the plot |

Andrew Hipp

`plot.rankedPartitionedRAD`

,
`locus.dist`

1 2 3 4 5 6 | ```
data(oak.rads)
data(oak.tree)
plot.locus.dist(locus.dist(oak.rads, proportional = TRUE), oak.tree)
# and now a nicer-looking plot:
plot.locus.dist(locus.dist(oak.rads, proportional = TRUE, upper = TRUE),
ladderize(oak.tree), trW = 1, labelsW = 1, scalar = 3)
``` |

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