https://github.com/japhir/geologictimescale
Read in the GTS as a csv, then use ggplot2 in R to make a timescale. Use patchwork to add it to your figures.
https://github.com/japhir/geologictimescale
geology ggplot2 r time timescale
Last synced: 6 months ago
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Read in the GTS as a csv, then use ggplot2 in R to make a timescale. Use patchwork to add it to your figures.
- Host: GitHub
- URL: https://github.com/japhir/geologictimescale
- Owner: japhir
- License: gpl-3.0
- Created: 2019-03-06T18:58:56.000Z (over 7 years ago)
- Default Branch: master
- Last Pushed: 2022-07-22T08:10:48.000Z (about 4 years ago)
- Last Synced: 2025-04-19T18:22:03.586Z (over 1 year ago)
- Topics: geology, ggplot2, r, time, timescale
- Language: R
- Homepage:
- Size: 800 KB
- Stars: 3
- Watchers: 1
- Forks: 1
- Open Issues: 0
-
Metadata Files:
- Readme: README.org
- License: LICENSE.md
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README
#+title: Make a nice Geologic Time Scale
#+property: header-args:R :session *R:GTS* :exports both :results output :eval no-export
In this repository I create a nice PDF on A3 size to print the Geologic Time Scale on a linear scale, so that it doesn't seem like the recent time periods took the same amount of time as the Precambrian.
I had to copy over all the colours and age ranges, because the official tools only provide a PDF.
If you want to use this figure for your own plots you can either:
1. load in the ~GTS_widths.csv~ file and plot it yourself
#+begin_src R
library(readr)
GTS <- read_csv("https://github.com/japhir/GeologicTimeScale/raw/master/GTS_widths.csv")
# create plot yourself
#+end_src
2. load in the ~gts_plot.rds~ file and tweak the plot itself.
#+begin_src R
library(ggplot2)
library(readr)
gts <- read_rds("https://github.com/japhir/GeologicTimeScale/raw/master/out/gts_plot.rds")
#+end_src
I prefer to read in the data, filter out what I want (e.g., only Epochs), then make the plot full-sized and add it to the data with [[https://patchwork.data-imaginist.com/][patchwork]].
*NOTE: it's probably much better to use a full-fledged package to add the Geologic Time Scale to your plots, e.g. using the [[https://github.com/willgearty/deeptime/][deeptime]] package!*
* full workflow
load libraries
#+begin_src R
library(dplyr)
library(ggplot2)
library(readr)
#+end_src
Read in my weird data frame
#+begin_src R
GTS <- read_csv("https://github.com/japhir/GeologicTimeScale/raw/master/GTS_widths.csv")
#+end_src
Create plot of "data"
#+begin_src R :results output graphics file :file imgs/iris.png :width 800 :height 500
dataplot <- iris |>
# create fake ages
mutate(age = rep(seq(0, 44, length.out = 50), 3)) |>
ggplot(aes(x = age, y = Petal.Length, colour = Species)) +
geom_point() +
geom_line()
dataplot
#+end_src
#+RESULTS:
[[file:imgs/iris.png]]
Now create the desired subset of the GTS plot
#+begin_src R :results output graphics file :file imgs/gts_data.png :width 800 :height 80
gtsplot <- GTS |>
# subset it to only show Periods
filter(type == "Period") |>
# filter to our time range
filter(top < 55) |>
# rectangles for each period
ggplot() +
geom_rect(aes(ymin = start, ymax = end, xmin = top, xmax = bot, fill = col),
show.legend = FALSE, col = "black") +
# make sure that the fill colour is given by our hex colours
scale_fill_identity() +
# add period names
geom_text(aes(x = meanage, y = meanwidth, label = name, size = fontsize * .5,
## angle = fontangle,
col = fontcolor, fontface = fontface)) +
# make sure the font size is set to your liking
scale_size_identity() +
scale_colour_identity() +
# add axis label for age axis
labs(x = "Age (millions of years ago)") +
theme(
# remove gray panel
panel.grid = element_blank(),
panel.background = element_blank(),
# remove y axis entirely
axis.line.y = element_blank(),
axis.title.y = element_blank(),
axis.text.y = element_blank(),
axis.ticks.y = element_blank()) +
coord_cartesian(xlim = c(0, 40))
gtsplot
#+end_src
#+RESULTS:
[[file:imgs/gts_data.png]]
And to combine the two, make sure they have precisely the same x axis and then join them together using patchwork.
#+begin_src R :results output graphics file :file imgs/gts_plus_data.png :width 800 :height 800
library(patchwork)
(dataplot +
# make sure that it has precisely the same x axis range
coord_cartesian(xlim = c(0, 40)) +
# then remove the redundant x-axis from the data
theme(axis.text.x = element_blank(), axis.title.x = element_blank())) /
# and add the gts beneath the data, at a smaller size
gtsplot + plot_layout(heights = c(1, .05))
#+end_src
#+RESULTS:
[[file:imgs/gts_plus_data.png]]
* contributing
If you spot any errors, please feel free to file an issue or write a pull request!
* copying
I've licensed the code with GPL-3, but the underlying data is copyright of the Geologic Time Scale at https://timescalefoundation.org/