deeptime (version 2.2.0)

gggeo_scale: Add a geologic scale below ggplots using grid

Description

This function takes a ggplot object and adds a geologic time scale at the specified side using the grid and gtable packages.

If custom data is provided (with dat), it should consist of at least 3 columns of data. See data(periods) for an example.

• The name column lists the names of each time interval. These will be used as labels if no abbreviations are provided.

• The max_age column lists the oldest boundary of each time interval.

• The min_age column lists the youngest boundary of each time interval.

• The abbr column is optional and lists abbreviations that may be used as labels.

• The color column is also optional and lists a hex color code (which can be obtained with rgb()) for each time interval.

Usage

gggeo_scale(obj, ...)
# S3 method for gtable
gggeo_scale(
  obj,
  lims,
  dat = "periods",
  fill = NULL,
  color = "black",
  alpha = 1,
  height = unit(2, "line"),
  pos = "bottom",
  lab = TRUE,
  rot = 0,
  abbrv = TRUE,
  skip = c("Quaternary", "Holocene", "Late Pleistocene"),
  size = 5,
  lwd = 0.25,
  margin = unit(0, "line"),
  neg = FALSE,
  bord = c("left", "right", "top", "bottom"),
  center_end_labels = FALSE,
  ...
)
# S3 method for ggplot
gggeo_scale(
  obj,
  dat = "periods",
  fill = NULL,
  color = "black",
  alpha = 1,
  height = unit(2, "line"),
  pos = "bottom",
  lab = TRUE,
  rot = 0,
  abbrv = TRUE,
  skip = c("Quaternary", "Holocene", "Late Pleistocene"),
  size = 5,
  lwd = 0.25,
  margin = unit(0, "line"),
  neg = FALSE,
  bord = c("left", "right", "top", "bottom"),
  center_end_labels = FALSE,
  ...
)
# S3 method for geo_scale
gggeo_scale(
  obj,
  dat = "periods",
  fill = NULL,
  color = "black",
  alpha = 1,
  height = unit(2, "line"),
  pos = "bottom",
  lab = TRUE,
  rot = 0,
  abbrv = TRUE,
  skip = c("Quaternary", "Holocene", "Late Pleistocene"),
  size = 5,
  lwd = 0.25,
  margin = unit(0, "line"),
  neg = FALSE,
  bord = c("left", "right", "top", "bottom"),
  center_end_labels = FALSE,
  ...
)
# S3 method for geo_scale
print(x, ...)

Value

A geo_scale object. Basically a gtable object but with the axis limits included.

Arguments

obj

An object of class ggplot, gtable, or geo_scale (as produced by this function).

...

further arguments passed to grid::grid.draw().

lims

The limits of the axis of the desired side of the plot. Only required if using a gtable object not created by this function.

dat

Either A) a string indicating a built-in dataframe with interval data from the ICS ("periods", "epochs", "stages", "eons", or "eras"), B) a string indicating a timescale from macrostrat (see list here: https://macrostrat.org/api/defs/timescales?all), or C) a custom dataframe of time interval boundaries (see Details).

fill

The fill color of the boxes. The default is to use the colors included in dat. If a custom dataset is provided with dat without color and without fill, a greyscale will be used. Custom fill colors can be provided with this option and will be recycled if/as necessary.

color

The outline color of the interval boxes.

alpha

The transparency of the fill colors.

height

The height (or width if pos is left or right) of the scale.

pos

Which side to add the scale to (left, right, top, or bottom). First letter may also be used.

lab

Whether to include labels.

rot

The amount of counter-clockwise rotation to add to the labels (in degrees).

abbrv

If including labels, whether to use abbreviations instead of full interval names.

skip

A vector of interval names indicating which intervals should not be labeled.

size

Label size.

lwd

Line width.

margin

The width of the margin around the returned object (can be a vector of length 4).

neg

Set this to true if your x-axis is using negative values.

bord

A vector specifying on Which sides of the scale to add borders (same options as pos).

center_end_labels

Should labels be centered within the visible range of intervals at the ends of the axis?

x

An object of class geo_scale.

Life cycle

This function is deprecated in favor of coord_geo() as of deeptime version 1.0.0. It will be removed in a future release.

Examples

library(ggplot2)
# bottom scale by default
p <- ggplot() +
  geom_point(aes(y = runif(1000, 0, 8), x = runif(1000, 0, 1000))) +
  scale_x_reverse() +
  coord_cartesian(xlim = c(1000, 0), ylim = c(0, 8), expand = FALSE) +
  theme_classic()
gggeo_scale(p)

# can specify any side of the plot
p <- ggplot() +
  geom_point(aes(x = runif(1000, 0, 8), y = runif(1000, 0, 1000))) +
  scale_y_reverse() +
  coord_cartesian(xlim = c(0, 8), ylim = c(1000, 0), expand = FALSE) +
  theme_classic()
gggeo_scale(p, pos = "left", rot = 90)

# can add multiple scales
p <- ggplot() +
  geom_point(aes(y = runif(1000, 0, 8), x = runif(1000, 0, 100))) +
  scale_x_reverse() +
  coord_cartesian(xlim = c(100, 0), ylim = c(0, 8), expand = FALSE) +
  theme_classic()
p <- gggeo_scale(p, abbrv = FALSE)
p <- gggeo_scale(p, dat = "epochs", height = unit(4, "lines"), rot = 90,
                 size = 2.5, abbrv = FALSE)
gggeo_scale(p, dat = "stages", height = unit(4, "lines"), rot = 90,
            size = 2.5, abbrv = FALSE)
if (FALSE) {
# intervals on both sides for different timescales (ICS stages vs North
# American Land Mammal Ages)
p <- ggplot() +
  geom_point(aes(x = runif(1000, 0, 10), y = runif(1000, 0, 65))) +
  scale_y_reverse() +
  coord_cartesian(xlim = c(0, 10), ylim = c(65, 0), expand = FALSE) +
  theme_classic()
p <- gggeo_scale(p, dat = "stages", pos = "left", height = unit(4, "lines"),
  size = 2.5, abbrv = FALSE)
gggeo_scale(p, dat = "North American Land Mammal Ages",
            pos = "right", height = unit(4, "lines"),
            size = 2.5, abbrv = FALSE)
}

# can add scales to a faceted plot
# use gggeo_scale_old() if you have more than one column
df <- data.frame(
  x = runif(1000, 0, 541), y = runif(1000, 0, 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(541, 0), ylim = c(0, 8), expand = FALSE) +
  theme_classic() +
  facet_wrap(~z, ncol = 1)
gggeo_scale(p)

# can even add a scale to a phylogeny (using ggtree)
if (FALSE) { # require(ggtree)
library(phytools)
library(ggtree)
tree <- pbtree(b = .03, d = .01, n = 100)
p <- ggtree(tree) +
  coord_cartesian(xlim = c(-500, 0), ylim = c(-2, 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)
}