In willgearty/deeptime: Plotting Tools for Anyone Working in Deep Time

knitr::opts_chunk$set(collapse = TRUE, fig.width = 7, fig.height = 5, fig.align = "center")

`coord_geo()` is also designed to work smoothly with phylogenies that are plotted with the [ggtree](https://www.bioconductor.org/packages/ggtree) package. First let's load some important packages. wzxhzdk:1 ## Timescales and phylogenies Now, let's plot some phylogenies with timescales! Note that by default the time axis increases toward the tips for trees plotted with `ggtree()`, so you must use the `revts()` function from [ggtree](https://www.bioconductor.org/packages/ggtree) to change the x-axis values to increasing negative values. Note that once you've done this, you will need to set `neg = TRUE` in `coord_geo()`. Furthermore, any time axis limits that you set will need to be negative. Here we also use the `scale_x_continuous()` function to relabel the negative x-axis values with positive labels. wzxhzdk:2 ### Phylogenies with only fossil taxa Many phylogenies only have fossil taxa in them (i.e., non-ultrametric). These can be handled by `coord_geo()` by using `position_nudge()` function. In most cases, you will want to nudge the time axis values (in this case, the x-axis) by the `root.time` of your phylogeny. Also, note that we have modified `plot.margin` here to accommodate the stacked timescale. wzxhzdk:3 ## Circular phylogenies Phylogenies can be plotted in a circular layout with a timescale background using the `coord_geo_radial()` function. It works just like `coord_geo()` and has many of the same arguments. You can use the `expand` argument in `scale_x_continuous()` to add space at either end of the timescale. You can use the `expand` argument in `scale_y_continuous()` to add space to either side of the phylogeny to prevent the tips from overlapping with the `pie` edges. Note that `coord_geo_radial()` only works with ggplot2 version 3.5.0 and higher. For other versions of ggplot2, you can use `coord_geo_polar()`. wzxhzdk:4

### Circular phylogenies with "stacked" timescales Timescales can even be "stacked" like with `coord_geo()`, although the stacking occurs in a circular fashion. We also use the `prop`, `start`, `end`, and `direction` arguments to specify how the different timescales are oriented and split within the polar space. wzxhzdk:5

### Disclaimer Note that `coord_geo_radial()` has been tested with the plotting of ultrametric and non-ultrametric phylogenies with `ggtree::ggtree()`, but it may have unexpected behavior when combined with other functions from [ggtree](https://www.bioconductor.org/packages/ggtree). Furthermore, `coord_geo_radial()` may be useful (albeit perhaps abstract) for plotting other types of data, but this has not been investigated.

willgearty/deeptime documentation built on April 5, 2024, 3:24 a.m.