This function provides a general interface to plot `phylo4d`

object
(i.e. phylogenetic tree and data).

1 2 3 4 5 6 7 8 9 10 11 12 13 | ```
multiplot.phylo4d(p4d, trait = names(tdata(p4d)), center = TRUE,
scale = TRUE, plot.type = "barplot", tree.ladderize = FALSE,
tree.type = "phylogram", tree.ratio = NULL, tree.xlim = NULL,
tree.open.angle = 0, tree.open.crown = TRUE, show.tip = TRUE,
tip.labels = NULL, tip.col = "black", tip.cex = 1, tip.font = 3,
tip.adj = 0, data.xlim = NULL, bar.lwd = 10, bar.col = "grey35",
show.data.axis = TRUE, dot.col = "black", dot.pch = 20, dot.cex = 2,
cell.col = white2red(100), show.color.scale = TRUE, show.trait = TRUE,
trait.labels = NULL, trait.col = "black", trait.cex = 1,
trait.font = 1, trait.bg.col = "grey90", error.bar.sup = NULL,
error.bar.inf = NULL, error.bar.col = 1, show.box = FALSE,
grid.vertical = TRUE, grid.horizontal = FALSE, grid.col = "grey25",
grid.lty = "dashed", ...)
``` |

`p4d` |
a |

`trait` |
the traits in the |

`center` |
a logical indicating whether traits values should be centered. |

`scale` |
a logical indicating whether traits values should be scaled. |

`plot.type` |
a character string specifying the type of plot for traits data.
Can be " |

`tree.ladderize` |
a logical indicating whether the tree should be (right) ladderized. |

`tree.type` |
a character string specifying the type of phylogeny to be drawn.
Can be " |

`tree.ratio` |
a numeric value in [0, 1] giving the proportion of width of the figure for the tree. |

`tree.xlim` |
a numeric vector of length 2 giving the limits of the x-axis for the tree. If |

`tree.open.angle` |
a numeric value giving the angle in degrees left blank if |

`tree.open.crown` |
a logical indicating whether the crowns should be drawn following the value
of |

`show.tip` |
logical indicating whether tips labels should be drawn. |

`tip.labels` |
character vector to label the tips.
If |

`tip.col` |
a vector of R colors to use for the tips labels. Recycled if necessary. |

`tip.cex` |
a numeric vector to control character size of the tips labels. Recycled if necessary. |

`tip.font` |
an integer vector specifying the type of font for the tips labels: 1 (plain text), 2 (bold), 3 (italic), or 4 (bold italic). Recycled if necessary. |

`tip.adj` |
a vector of numeric in [0, 1] to control tips labels justification: 0 (left-justification), 0.5 (centering), or 1 (right-justification). Recycled if necessary. |

`data.xlim` |
numeric vector of length 2 or matrix giving the x coordinates range for the barplots/dotplots (see Details). |

`bar.lwd` |
a vector of numeric giving bar widths of the barplot(s). Recycled along the tips, reapeated for each trait. |

`bar.col` |
a vector of R colors to use for the bars. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning (see Details) |

`show.data.axis` |
logical indicating whether barplots/dotplots axes should be drawn. |

`dot.col` |
a vector of R colors to use for the points. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning (see Details) |

`dot.pch` |
a numerical vector of symbol to use for the points. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning (see Details) |

`dot.cex` |
a numerical vector. Character (or symbol) expansion for the points. Recycled along the tips, reapeated for each trait. The user can also provide a matrix for a finer tuning (see Details) |

`cell.col` |
a vector of colors for |

`show.color.scale` |
logical indicating whether color scale should be drawn. |

`show.trait` |
logical indicating whether traits labels should be drawn. |

`trait.labels` |
character vector to label the traits.
If |

`trait.col` |
a vector of R colors to use for the traits labels. Recycled if necessary. |

`trait.cex` |
a numeric vector to control character size of the trait labels. Recycled if necessary. |

`trait.font` |
an integer vector specifying the type of font for the traits labels: 1 (plain text), 2 (bold), 3 (italic), or 4 (bold italic). Recycled if necessary. |

`trait.bg.col` |
a vector of R colors to use for the background of the barplots. Recycled if necessary. |

`error.bar.sup` |
a matrix giving the superior limit for error bars. Columns and rows names must match with traits and tips labels, respectively. |

`error.bar.inf` |
a matrix giving the inferior limit for error bars. Columns and rows names must match with traits and tips labels, respectively. |

`error.bar.col` |
a vector of R colors to draw error bars. |

`show.box` |
a logical indicating whether a box should be drawn around the plots. |

`grid.vertical` |
a logical incating whether vertical lines of the grid should be drawn. |

`grid.horizontal` |
a logical incating whether horizontal lines of the grid should be drawn. |

`grid.col` |
a vector of R colors to use for the lines of the grid. |

`grid.lty` |
the lines type of the grid. Possibly a vector. |

`...` |
further arguments to be passed to |

phylosignal documentation built on Jan. 10, 2018, 5:03 p.m.

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