deeptime

Overview

deeptime extends the functionality of other plotting packages (notably {ggplot2}) to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of deeptime is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.

Installation

# get the stable version from CRAN
install.packages("deeptime")

# or get the development version from github
# install.packages("devtools")
devtools::install_github("willgearty/deeptime")

Usage

Load packages

library(deeptime)
library(ggplot2)
library(dplyr)

Add one or more timescales to virtually any ggplot2 plot!

The main function of deeptime is coord_geo(), which functions just like coord_trans() from {ggplot2}. You can use this function to add highly customizable timescales to a wide variety of ggplots.

library(divDyn)
data(corals)

# this is not a proper diversity curve but it gets the point across
coral_div <- corals %>% filter(stage != "") %>%
  group_by(stage) %>%
  summarise(n = n()) %>%
  mutate(stage_age = (stages$max_age[match(stage, stages$name)] +
                        stages$min_age[match(stage, stages$name)])/2)
ggplot(coral_div) +
  geom_line(aes(x = stage_age, y = n)) +
  scale_x_reverse("Age (Ma)") +
  ylab("Coral Genera") +
  coord_geo(xlim = c(250, 0), ylim = c(0, 1700)) +
  theme_classic(base_size = 16)

Lots of timescales available!

# Load packages
library(gsloid)

# Plot two different timescales
ggplot(lisiecki2005) +
  geom_line(aes(x = d18O, y = Time / 1000), orientation = "y") +
  scale_y_reverse("Time (Ma)") +
  scale_x_reverse("\u03B418O") +
  coord_geo(
    dat = list("Geomagnetic Polarity Chron",
               "Planktic foraminiferal Primary Biozones"),
    xlim = c(6, 2), ylim = c(5.5, 0), pos = list("l", "r"),
    rot = 90, skip = "PL4", size = list(5, 4)
  ) +
  theme_classic(base_size = 16)

Super flexible, supports multiple layouts, and works great with other packages!

# Load packages
library(ggtree)
library(rphylopic)

# Get vertebrate phylogeny
library(phytools)
data(vertebrate.tree)

vertebrate.tree$tip.label[vertebrate.tree$tip.label ==
                            "Myotis_lucifugus"] <- "Vespertilioninae"
vertebrate_data <- data.frame(species = vertebrate.tree$tip.label,
                              name = vertebrate.tree$tip.label)

# Plot the phylogeny with a timescale
revts(ggtree(vertebrate.tree, size = 1)) %<+%
  vertebrate_data +
  geom_phylopic(aes(name = name), size = 25) +
  scale_x_continuous("Time (Ma)", breaks = seq(-500, 0, 100),
                     labels = seq(500, 0, -100), limits = c(-500, 0),
                     expand = expansion(mult = 0)) +
  scale_y_continuous(guide = NULL) +
  coord_geo_radial(dat = "periods", end = 0.5 * pi) +
  theme_classic(base_size = 16)

Does lots of other things too!

Plot fossil occurence ranges

library(palaeoverse)

# Filter occurrences
occdf <- subset(tetrapods, accepted_rank == "genus")
occdf <- subset(occdf, accepted_name %in%
                  c("Eryops", "Dimetrodon", "Diadectes", "Diictodon",
                    "Ophiacodon", "Diplocaulus", "Benthosuchus"))

# Plot occurrences
ggplot(data = occdf) +
  geom_points_range(aes(x = (max_ma + min_ma)/2, y = accepted_name)) +
  scale_x_reverse(name = "Time (Ma)") +
  ylab(NULL) +
  coord_geo(pos = list("bottom", "bottom"), dat = list("stages", "periods"),
            abbrv = list(TRUE, FALSE), expand = TRUE, size = "auto") +
  theme_classic(base_size = 16)

Use standardized geological patterns

# Load packages
library(rmacrostrat)
library(ggrepel)

# Retrieve the Macrostrat units in the San Juan Basin column
san_juan_units <- get_units(column_id = 489, interval_name = "Cretaceous")

# Specify x_min and x_max in dataframe
san_juan_units$x_min <- 0
san_juan_units$x_max <- 1
# Tweak values for overlapping units
san_juan_units$x_max[10] <- 0.5
san_juan_units$x_min[11] <- 0.5

# Add midpoint age for plotting
san_juan_units$m_age <- (san_juan_units$b_age + san_juan_units$t_age) / 2

# Get lithology definitions
liths <- def_lithologies()

# Get the primary lithology for each unit
san_juan_units$lith_prim <- sapply(san_juan_units$lith, function(df) {
  df$name[which.max(df$prop)]
})

# Get the pattern codes for those lithologies
san_juan_units$pattern <- factor(liths$fill[match(san_juan_units$lith_prim, liths$name)])

# Plot with pattern fills
ggplot(san_juan_units, aes(ymin = b_age, ymax = t_age,
                           xmin = x_min, xmax = x_max)) +
  # Plot units, patterned by rock type
  geom_rect(aes(fill = pattern), color = "black") +
  scale_fill_geopattern(name = NULL,
                        breaks = factor(liths$fill), labels = liths$name) +
  # Add text labels
  geom_text_repel(aes(x = x_max, y = m_age, label = unit_name),
                  size = 3.5, hjust = 0, force = 2,
                  min.segment.length = 0, direction = "y",
                  nudge_x = rep_len(x = c(2, 3), length.out = 17)) +
  # Add geological time scale
  coord_geo(pos = "left", dat = list("stages"), rot = 90) +
  # Reverse direction of y-axis
  scale_y_reverse(limits = c(145, 66), n.breaks = 10, name = "Time (Ma)") +
  # Remove x-axis guide and title
  scale_x_continuous(NULL, guide = NULL) +
  # Choose theme and font size
  theme_classic(base_size = 14) +
  # Make tick labels black
  theme(legend.position = "bottom", legend.key.size = unit(1, 'cm'),
        axis.text.y = element_text(color = "black"))