deeptime

Tools (currently just one function) to help with plotting data over long time intervals.

To install

library(devtools)
install_github("willgearty/deeptime")

To use

Note #1: This function does not expand your axes (yet), which may result in the scale overlapping with your data. Please use caution and set your axis limits manually to account for this.

Note #2: Make sure to include any fill or color scales beforehand, as you will not be able to modify these attributes for your main plot after applying this function.

Default scale on bottom axis

library(deeptime)
library(ggplot2)
p <- ggplot() +
  geom_point(aes(y = runif(1000, .5, 8), x = runif(1000, 0, 1000))) +
  scale_x_reverse() +
  coord_cartesian(xlim = c(0, 1000), ylim = c(0,8), expand = FALSE) +
  theme_classic()
gggeo_scale(p)

Move scale to left axis

p <- ggplot() +
  geom_point(aes(x = runif(1000, .5, 8), y = runif(1000, 0, 541))) +
  scale_y_reverse() +
  coord_cartesian(xlim = c(0, 8), ylim = c(0,541), expand = FALSE) +
  theme_classic()
gggeo_scale(p, pos = "left", rot = 90)

Stack multiple scales (e.g. periods, epochs, stages)

p <- ggplot() +
  geom_point(aes(y = runif(1000, 1, 8), x = runif(1000, 0, 1000))) +
  scale_x_reverse() +
  coord_cartesian(xlim = c(0, 100), ylim = c(0,8), expand = FALSE) +
  theme_classic()
p <- gggeo_scale(p, height = .03, abbrv = FALSE)
p <- gggeo_scale(p, dat = "epochs", gap = .03, height = .1, rot = 90, size = 2.5, abbrv = FALSE)
gggeo_scale(p, dat = "stages", gap = .13, height = .1, rot = 90, size = 2.5, abbrv = FALSE)

Scale on faceted plot

df <- data.frame(x = runif(1000, 0, 541), y = runif(1000, .5, 8), z = sample(c(1,2,3,4), 1000, TRUE))
p <- ggplot(df) +
    geom_point(aes(x, y)) +
    scale_x_reverse() +
    coord_cartesian(xlim = c(0, 541), ylim = c(0,8), expand = FALSE) +
    theme_classic() +
    facet_wrap(~z, nrow = 2)
gggeo_scale(p)

Add scale to phylogeny

library(phytools)
library(ggtree)
tree <- pbtree(b = .03, d = .01,  n=100)
p <- ggtree(tree) +
  coord_cartesian(xlim = c(0,-500), ylim = c(-10,Ntip(tree)), expand = FALSE) +
  scale_x_continuous(breaks=seq(-500,0,100), labels=abs(seq(-500,0,100))) +
  theme_tree2()
p <- revts(p)
gggeo_scale(p, neg = TRUE)

Add scale to a phylogeny with only fossil taxa

library(phytools)
library(ggtree)
tree<-read.tree(text="(A:3,(B:2,(C:5,D:3):2):3);")
tree$root.time<-20
p <- ggtree(tree, position = position_nudge(x = -tree$root.time)) +
  coord_cartesian(xlim = c(0,-25), ylim = c(.5,Ntip(tree)), expand = FALSE) +
  scale_x_continuous(breaks=seq(-50,50,10), labels=abs(seq(-50,50,10))) +
  theme_tree2()
p <- gggeo_scale(p, neg = TRUE, skip = NULL, abbrv = FALSE)
gggeo_scale(p, dat = "epochs", gap = .05, neg = TRUE, skip = "Holocene", abbrv = FALSE, size = 4)