deeptime

Overview

Extends the functionality of other plotting packages like ggplot2 and lattice 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)

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.

Default scale on bottom axis

library(divDyn)
library(tidyverse)
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()

Scale on left axis

library(gsloid)
ggplot(lisiecki2005) +
  geom_line(aes(x = d18O, y = Time/1000), orientation = "y") +
  scale_y_reverse("Time (Ma)") +
  scale_x_reverse() +
  coord_geo(dat = "Geomagnetic Polarity Chron", xlim = c(6,2), ylim = c(6,0), pos = "left", rot = 90) +
  theme_classic()

Stack multiple scales (e.g. periods and eras)

Specify multiple scales by giving a list for pos. Scales are added from the inside to the outside. Other arguments can be lists or single values (either of which will be recycled if necessary).

# uses the coral diversity data from above
ggplot(coral_div) +
  geom_line(aes(x = stage_age, y = n)) +
  scale_x_reverse("Age (Ma)") +
  ylab("Coral Genera") +
  coord_geo(dat = list("periods", "eras"), xlim = c(250, 0), ylim = c(0, 1700),
            pos = list("b", "b"), abbrv = list(TRUE, FALSE)) +
  theme_classic()

Show intervals from different scales (e.g. Geochrons vs. Foram biozones)

# uses the oxygen isotope data from above
ggplot(lisiecki2005) +
  geom_line(aes(x = d18O, y = Time/1000), orientation = "y") +
  scale_y_reverse("Time (Ma)") +
  scale_x_reverse() +
  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()

Scale on faceted plot

You can change on which facets the time scale is plotted by changing the scales argument in facet_wrap().

# uses the coral occurrence data from above
coral_div_diet <- corals %>% filter(stage != "") %>%
  group_by(diet, 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_diet) +
  geom_line(aes(x = stage_age, y = n)) +
  scale_x_reverse("Age (Ma)") +
  ylab("Coral Genera") +
  coord_geo(xlim = c(250, 0)) +
  theme_classic() +
  facet_wrap(~diet, nrow = 3)

Scale on discrete axis

coord_geo() will automatically detect if your axis is discrete. The categories of the discrete axis (which can be reordered using the limits argument of scale_[x/y]_discrete()) should match the name column of the timescale data (dat). You can use the arguments of theme() and scale_[x/y]_discrete() to optionally remove the labels and tick marks.

# uses the coral occurrence data from above
coral_div_dis <- corals %>% filter(period != "") %>%
  group_by(diet, period) %>%
  summarise(n = n()) %>%
  mutate(period_age = (periods$max_age[match(period, periods$name)] + periods$min_age[match(period, periods$name)])/2) %>%
  arrange(-period_age)

ggplot(coral_div_dis) +
  geom_col(aes(x = period, y = n, fill = diet)) +
  scale_x_discrete("Period", limits = unique(coral_div_dis$period), labels = NULL, expand = expansion(add = .5)) +
  scale_y_continuous(expand = c(0,0)) +
  scale_fill_viridis_d() +
  ylab("Coral Genera") +
  coord_geo(expand = TRUE, skip = NULL, abbrv = FALSE) +
  theme_classic() +
  theme(axis.ticks.length.x = unit(0, "lines"))

Custom discrete scale

You can also supply your own pre-discretized scale data by setting the dat_is_discrete parameter to TRUE. You can even have one scale with auto-discretized ages and one scale with pre-discretized ages.

eras_custom <- data.frame(name = c("Mesozoic", "Cenozoic"), max_age = c(0.5, 3.5), min_age = c(3.5, 6.5), color = c("#67C5CA", "#F2F91D"))

ggplot(coral_div_dis) +
  geom_col(aes(x = period, y = n, fill = diet)) +
  scale_x_discrete(NULL, limits = unique(coral_div_dis$period), labels = NULL, expand = expansion(add = .5)) +
  scale_y_continuous(expand = c(0,0)) +
  scale_fill_viridis_d() +
  ylab("Coral Genera") +
  coord_geo(dat = list("periods", eras_custom), pos = c("b", "b"), expand = TRUE, skip = NULL, abbrv = FALSE, dat_is_discrete = list(FALSE, TRUE)) +
  theme_classic() +
  theme(axis.ticks.length.x = unit(0, "lines"))

Resize labels to fit inside interval rectangles

coord_geo() can use the ggfittext package to resize labels. This can be enabled by setting size to "auto". Additional arguments can be passed to geom_fit_text() as a list using the fittext_args argument.

ggplot(coral_div) +
  geom_line(aes(x = stage_age, y = n)) +
  scale_x_reverse("Age (Ma)") +
  ylab("Coral Genera") +
  coord_geo(dat = "periods", xlim = c(250, 0), ylim = c(0, 1700),
            abbrv = FALSE, size = "auto", fittext_args = list(size = 20)) +
  theme_classic()

Add scale to a phylogeny

library(phytools)
library(ggtree)
data(mammal.tree)
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)

Add scale to a phylogeny with only fossil taxa

library(phytools)
library(ggtree)
library(paleotree)
data(RaiaCopesRule)
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))

Combine plots with timescales and plots without timescales

library(paleotree)
data(RaiaCopesRule)
p1 <- ggplot(ammoniteTraitsRaia) +
  geom_point(aes(x = Log_D, y = FD)) +
  labs(x = "Body size", y = "Suture complexity") +
  theme_classic()

p2 <- ggplot(ammoniteTraitsRaia) +
  geom_point(aes(x = Log_D, y = log_dur)) +
  labs(x = "Body size", y = "Stratigraphic duration (myr)") +
  theme_classic()

p3 <- ggtree(ammoniteTreeRaia, position = position_nudge(x = -ammoniteTreeRaia$root.time)) +
  coord_geo(xlim = c(-415,-66), ylim = c(-2,Ntip(ammoniteTreeRaia)), pos = "bottom",
            size = 4, abbrv = FALSE, neg = TRUE) +
  scale_x_continuous(breaks = seq(-425, -50, 25), labels = -seq(-425, -50, 25)) +
  theme_tree2() +
  theme(plot.margin = margin(7,11,7,11))

ggarrange2(ggarrange2(p1, p2, widths = c(2,1), draw = FALSE), p3, nrow = 2, heights = c(1,2))

Plot disparity through time

With ggplot

#make transformer
library(ggforce)
trans <- linear_trans(shear(.5, 0))

library(dispRity)
data(demo_data)
# prepare data to be plotted
crinoids <- as.data.frame(demo_data$wright$matrix[[1]][, 1:2])
crinoids$time <- "before extinction"
crinoids$time[demo_data$wright$subsets$after$elements] <- "after extinction"

square <- data.frame(V1 = c(-.6, -.6, .6, .6), V2 = c(-.4, .4, .4, -.4))

# plot data normally
ggplot() +
  geom_segment(data = data.frame(x = -.6, y = seq(-.4, .4,.2), xend = .6, yend = seq(-0.4, .4, .2)),
               aes(x = x, y = y, xend = xend, yend=yend), linetype = "dashed", color = "grey") +
  geom_segment(data = data.frame(x = seq(-.6, .6, .2), y = -.4, xend = seq(-.6, .6, .2), yend = .4),
               aes(x = x, y = y, xend = xend, yend=yend), linetype = "dashed", color = "grey") +
  geom_polygon(data = square, aes(x = V1, y = V2), fill = NA, color = "black") +
  geom_point(data = crinoids, aes(x = V1, y = V2), color = 'black') +
  coord_cartesian(expand = FALSE) +
  labs(x = "PCO1", y = "PCO2") +
  theme_classic() +
  facet_wrap(~time, ncol = 1, strip.position = "right") +
  theme(panel.spacing = unit(1, "lines"), panel.background = element_blank())

# plot data with transformation
ggplot() +
  geom_segment(data = data.frame(x = -.6, y = seq(-.4, .4,.2), xend = .6, yend = seq(-0.4, .4, .2)),
               aes(x = x, y = y, xend = xend, yend=yend), linetype = "dashed", color = "grey") +
  geom_segment(data = data.frame(x = seq(-.6, .6, .2), y = -.4, xend = seq(-.6, .6, .2), yend = .4),
               aes(x = x, y = y, xend = xend, yend=yend), linetype = "dashed", color = "grey") +
  geom_polygon(data = square, aes(x = V1, y = V2), fill = NA, color = "black") +
  geom_point(data = crinoids, aes(x = V1, y = V2), color = 'black') +
  coord_trans_xy(trans = trans, expand = FALSE) +
  labs(x = "PCO1", y = "PCO2") +
  theme_classic() +
  facet_wrap(~time, ncol = 1, strip.position = "right") +
  theme(panel.spacing = unit(1, "lines"), panel.background = element_blank())

With base R/lattice

# use same data as above
# plot data
crinoids$time <- factor(crinoids$time)
disparity_through_time(time~V1*V2, data = crinoids, groups = time, aspect = c(1.5,2), xlim = c(-.6,.6), ylim = c(-.5,.5),
                       col.regions = "lightgreen", col.point = c("red","blue"))