Adding geological timescales to phylogenies

coord_geo() is also designed to work smoothly with phylogenies that are plotted with the ggtree package. First let’s load some important packages.

# 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 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.

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.

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.

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()

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.

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()

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. 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:

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()

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.

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()

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, so we use an end value that is just slightly smaller than the start value. 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.

revts(ggtree(mammal.tree)) +
  coord_geo_radial(dat = "stages", fill = c("grey90", "grey95"), end = 1.49 * pi) +
  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"))

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.