gggeo_scale: Add a geologic scale below ggplots using _grid_

In deeptime: Plotting Tools for Anyone Working in Deep Time

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 class '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 class '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 class '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 class 'geo_scale'
print(x, ...)

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.

Value

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

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)
## Not run: 
# 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)

## End(Not run)

# 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)

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)

deeptime documentation built on Oct. 30, 2024, 9:08 a.m.