Adding geological timescales to phylogenies"
In 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_polar()` function. It works just like `coord_geo()` and has many of the same arguments. Note that labels for the intervals are not currently implemented (because of the potential mess this could cause if it was automated). wzxhzdk:4 ### Circular phylogenies with "stacked" timescales Timescales can even be "stacked" like with `coord_geo()`, although the stacking occurs in a circular fashion. In this case, we use `scale_y_continuous()` to add a small expansion to the y-axis (which is now the theta axis) so the numbers don't overlap with the phylogeny. We also use the `prop` and `start` arguments to specify how the different timescales are oriented and split within the polar space. The `axis.line.r`, `axis.text.r`, `axis.ticks.r`, and `axis.ticks.length.r` ggplot2 `theme()` elements can be modified just like their x and y counterparts to change the appearance of the radial axis. The default settings work well for a horizontal axis pointing towards the right, but these theme settings will need to be modified for other orientations such as in this example. wzxhzdk:5 ### Disclaimer Note that `coord_geo_polar()` 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_polar()` may be useful (albeit perhaps abstract) for plotting other types of data, but this has not been investigated.