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https://github.com/willgearty/deeptime
Plotting Tools for Anyone Working in Deep Time
https://github.com/willgearty/deeptime
geology ggplot2 paleontology r visualization
Last synced: 3 days ago
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Plotting Tools for Anyone Working in Deep Time
- Host: GitHub
- URL: https://github.com/willgearty/deeptime
- Owner: willgearty
- License: gpl-3.0
- Created: 2018-10-10T23:22:08.000Z (about 6 years ago)
- Default Branch: master
- Last Pushed: 2024-10-25T13:48:05.000Z (2 months ago)
- Last Synced: 2024-10-30T02:36:30.199Z (about 2 months ago)
- Topics: geology, ggplot2, paleontology, r, visualization
- Language: R
- Homepage: https://williamgearty.com/deeptime/
- Size: 95.1 MB
- Stars: 85
- Watchers: 4
- Forks: 8
- Open Issues: 8
-
Metadata Files:
- Readme: README.md
- Changelog: NEWS.md
- License: LICENSE.md
Awesome Lists containing this project
- awesome-ggplot2 - deeptime
README
# deeptime 
[](https://github.com/willgearty/deeptime/actions/workflows/R-CMD-check.yaml)
[](https://app.codecov.io/gh/willgearty/deeptime)
[](https://zenodo.org/badge/latestdoi/152502088)
[](https://CRAN.R-project.org/package=deeptime)
[](https://cran.r-project.org/package=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
```r
# 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
```r
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.
```r
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!
```r
# 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!
```r
# 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
```r
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
```r
# 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() +
# 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)) +
# Reverse direction of y-axis
scale_y_reverse(limits = c(145, 66), n.breaks = 10, name = "Time (Ma)") +
# Theming
theme_classic(base_size = 16) +
theme(legend.position = "none",
axis.line.x = element_blank(),
axis.title.x = element_blank(),
axis.text.x = element_blank(),
axis.ticks.x = element_blank()) +
# Add geological time scale
coord_geo(pos = "left", dat = list("stages"), rot = 90)
```
