---
title: "Adding geological timescales to phylogenies"
output: rmarkdown::html_vignette
vignette: >
  %\VignetteIndexEntry{Adding geological timescales to phylogenies}
  %\VignetteEngine{knitr::rmarkdown}
  %\VignetteEncoding{UTF-8}
---

```{r, include = FALSE}
knitr::opts_chunk$set(collapse = TRUE, fig.width = 7, fig.height = 5, fig.align = "center",
                      out.width = "100%")
```

<div style="text-align: justify">
`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.

```{r message = FALSE, warning = FALSE}
# Load deeptime
library(deeptime)
# Load other packages
library(ggplot2)
library(dplyr)
# Load ggtree
library(ggtree)
# Load phytools for some example data
library(phytools)
data(mammal.tree)
# Load paleotree for some example fossil data
library(paleotree)
data(RaiaCopesRule)
```

## 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.
```{r}
p <- ggtree(mammal.tree) +
  coord_geo(xlim = c(-75, 0), ylim = c(-2, Ntip(mammal.tree)),
            neg = TRUE, abbrv = FALSE) +
  scale_x_continuous(breaks = seq(-80, 0, 20), labels = abs(seq(-80, 0, 20))) +
  theme_tree2()
revts(p)
```

### 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.
```{r}
ggtree(ceratopsianTreeRaia,
       position = position_nudge(x = -ceratopsianTreeRaia$root.time)) +
  coord_geo(
    xlim = c(-163.5, -66), ylim = c(-2, Ntip(ceratopsianTreeRaia)),
    pos = list("bottom", "bottom"), skip = c("Paleocene", "Middle Jurassic"),
    dat = list("epochs", "periods"), abbrv = FALSE,
    size = list(4, 5), neg = TRUE, center_end_labels = TRUE
  ) +
  scale_x_continuous(breaks = -rev(epochs$max_age),
                     labels = rev(epochs$max_age)) +
  theme_tree2() +
  theme(plot.margin = margin(7, 11, 7, 11))
```

## 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.
```{r eval = FALSE}
revts(ggtree(mammal.tree)) +
  coord_geo_radial(dat = "stages") +
  scale_x_continuous(breaks = seq(-60, 0, 20), labels = abs(seq(-60, 0, 20)),
                     expand = expansion(mult = c(0.05, 0))) +
  scale_y_continuous(guide = NULL, expand = expansion(mult = c(0.01, 0.01))) +
  theme_classic()
```
<div class="figure">
<img src="phylogenies-1.png" alt="plot of phylogeny with a timescale in the background" width="100%" />
</div>

### 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.
```{r eval = FALSE}
revts(ggtree(mammal.tree)) +
  coord_geo_radial(
      dat = list("stages", "periods"), alpha = .5, lty = "dashed",
      prop = list(0.66, .34), start = 2 * pi, end = 1.75 * pi, direction = 1,
  ) +
  scale_x_continuous(breaks = seq(-60, 0, 20), labels = abs(seq(-60, 0, 20)),
                     expand = expansion(mult = c(0.05, 0))) +
  scale_y_continuous(guide = NULL, expand = expansion(mult = c(0.01, 0.01))) +
  theme_classic()
```

<div class="figure">
<img src="phylogenies-2.png" alt="plot of phylogeny with stacked timescales in the background" width="100%" />
</div>

### 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.

### Axis timescales on radial phylogenies
`coord_geo_radial()` is quite different from `coord_geo()`. Instead of adding a timescale to an axis, it adds the timescale to the entire (or part of the) background of the radial plot. In many cases, this may be useful. However, if you're annotating your plot with other text or shapes, these background colors may be distracting. Perhaps you'd rather just have the look of `coord_geo()` instead along the radial axis? Look no further than `guide_geo()`. By default, ggplot uses `guide_axis()` to style the radial axis of radial plots. However, we can replace this with time intervals using the `guide_geo()` function. Here's a brief example using the same mammal phylogeny from above:

```{r eval = FALSE}
revts(ggtree(mammal.tree)) +
  coord_radial(theta = "y", start = -0.5 * pi, end = 1.25 * pi) +
  scale_x_continuous(breaks = seq(-60, 0, 20), labels = abs(seq(-60, 0, 20)),
                     expand = expansion(mult = c(0.05, 0)),
                     guide = guide_geo("epochs", neg = TRUE, rot = -90,
                                       size = "auto",
                                       height = unit(1, "line"))) +
  scale_y_continuous(guide = NULL, expand = expansion(mult = c(0.01, 0.01))) +
  theme_classic()
```

<div class="figure">
<img src="phylogenies-3.png" alt="plot of phylogeny with guide_geo" width="100%" />
</div>

You'll notice that the tick marks and labels are now missing. This is because `guide_geo()` only adds the intervals, not the rest of the axis stuff. Don't worry, we can add those in too using `guide_axis_stack()` and `guide_axis()`. In most cases you probably want to set the `spacing` to 0 (i.e., `unit(0, "line")`) so the different guides are glued together.

```{r eval = FALSE}
revts(ggtree(mammal.tree)) +
  coord_radial(theta = "y", start = -0.5 * pi, end = 1.25 * pi) +
  scale_x_continuous(breaks = seq(-60, 0, 20), labels = abs(seq(-60, 0, 20)),
                     expand = expansion(mult = c(0.05, 0)),
                     guide = guide_axis_stack(guide_geo("epochs", neg = TRUE,
                                                        rot = -90, size = "auto",
                                                        height = unit(1, "line")),
                                              guide_axis(),
                                              spacing = unit(0, "line"))) +
  scale_y_continuous(guide = NULL, expand = expansion(mult = c(0.01, 0.01))) +
  theme_classic()
```

<div class="figure">
<img src="phylogenies-4.png" alt="plot of phylogeny with stacked guides" width="100%" />
</div>

There they are! Hmm...after looking at all of these phylogenies with background colors, this one looks quite bare. Fortunately, we can use _both_ `coord_geo_radial()` and `guide_geo()` to make a phylogeny that really pops! However, since we're trying to avoid a distracting background, we'll set the fill colors to a light gray scale. We'll also adjust the `end` value for `coord_geo_radial()` to remove the empty space. Note that if the `start` and `end` values result in the same polar locations, the axis will be bumped to the margin, but we can override this with `r.axis.inside = TRUE`. This leaves a very small gap, but it's covered by the `guide_geo()` boxes. Finally, note that you can use `guide_geo()` within `scale_` functions and also within the `guides()` function.

```{r eval = FALSE}
revts(ggtree(mammal.tree)) +
  coord_geo_radial(dat = "stages", fill = c("grey90", "grey95"), end = 1.5 * pi,
                   r.axis.inside = TRUE) +
  scale_x_continuous(breaks = seq(-60, 0, 20), labels = abs(seq(-60, 0, 20)),
                     expand = expansion(mult = c(0.05, 0))) +
  scale_y_continuous(guide = NULL, expand = expansion(mult = c(0.01, 0.05))) +
  theme_classic() +
  guides(r = guide_axis_stack(guide_geo("epochs", neg = TRUE,
                                        rot = -90, size = "auto",
                                        height = unit(1, "line")),
                              guide_axis(),
                              spacing = unit(0, "line"))) +
  theme(axis.text.y = element_text(color = "black"))
```

<div class="figure">
<img src="phylogenies-5.png" alt="plot of phylogeny with stacked guides and coord_geo_radial" width="100%" />
</div>

Very cool! Note that `guide_geo()` can actually be used for any plot, but it basically does the same thing as `coord_geo()` for non-radial plots and generally requires more lines of code.

### Tip labels on radial phylogenies

__deeptime__ also provides a specialized geom, `geom_text_phylo()`, for adding tip labels to phylogenies plotted with `ggtree()`. It works similarly to `ggtree::geom_tiplab()`, `ggtree::geom_tiplab2()`, `ggtree::geom_nodelab()`, and `ggtree::geom_nodelab2()`. However, unlike those geoms, this geom is intended to work with all coordinate systems, including `coord_geo()`, `ggplot2::coord_radial()`, and `coord_geo_radial()`. For example, it can automatically adjust the angle and justification of the text based on its position in the plot. It can also be used to label only tips or only internal nodes. Here's a brief example using the same mammal phylogeny from above. Notice that we use `nudge_x = 2` to move the labels away from the tips a bit. We also use `plot.margin` to add some space around the plot so the labels aren't cut off.

```{r eval = FALSE}
revts(ggtree(mammal.tree)) +
    geom_text_phylo(nudge_x = 2) +
    coord_geo_radial(dat = "stages", fill = c("grey90", "grey95"), end = 1.5 * pi,
                     r.axis.inside = TRUE) +
    scale_x_continuous(breaks = seq(-60, 0, 20), labels = abs(seq(-60, 0, 20)),
                       expand = expansion(mult = c(0.05, 0))) +
    scale_y_continuous(guide = NULL, expand = expansion(mult = c(0.01, 0.05))) +
    theme_classic() +
    guides(r = guide_axis_stack(guide_geo("epochs", neg = TRUE,
                                          rot = -90, size = "auto",
                                          height = unit(1, "line")),
                                guide_axis(),
                                spacing = unit(0, "line"))) +
    theme(axis.text.y = element_text(color = "black"), plot.margin = margin(4,4,4,4, "lines"))
```

<div class="figure">
<img src="phylogenies-6.png" alt="plot of phylogeny with stacked guides, coord_geo_radial, and tip labels generated with geom_text_phylo" width="100%" />
</div>

`geom_text_phylo()` inherits all of the arguments from `ggplot2::geom_text()`, so you can modify the text size, color, font, etc. as you would with any other text geom. You can also use the `angle`, `hjust`, and `vjust` aesthetics to further customize the text orientation and justification.

</div>
