coord_geo: Transformed coordinate system with geological timescale

In deeptime: Plotting Tools for Anyone Working in Deep Time

Transformed coordinate system with geological timescale

Description

coord_geo behaves similarly to ggplot2::coord_trans() in that it occurs after statistical transformation and will affect the visual appearance of geoms. The main difference is that it also adds a geological timescale to the specified side(s) of the plot.

Usage

coord_geo(
  pos = "bottom",
  dat = "periods",
  xlim = NULL,
  ylim = NULL,
  xtrans = identity_trans(),
  ytrans = identity_trans(),
  clip = "on",
  expand = FALSE,
  fill = NULL,
  color = "black",
  alpha = 1,
  height = unit(2, "line"),
  lab = TRUE,
  lab_color = NULL,
  rot = 0,
  abbrv = TRUE,
  skip = c("Quaternary", "Holocene", "Late Pleistocene"),
  size = 5,
  lwd = 0.25,
  neg = FALSE,
  bord = c("left", "right", "top", "bottom"),
  center_end_labels = FALSE,
  dat_is_discrete = FALSE,
  fittext_args = list()
)

Arguments

pos	Which side to add the scale to (left, right, top, or bottom). First letter may also be used.
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 data.frame of time interval boundaries (see Details).
xlim, ylim	Limits for the x and y axes.
xtrans, ytrans	Transformers for the x and y axes. For more information see ggplot2::coord_trans().
clip	Should drawing be clipped to the extent of the plot panel? For more information see ggplot2::coord_trans().
expand	If FALSE, the default, limits are taken exactly from the data or xlim/ylim. If TRUE, adds a small expansion factor to the limits to ensure that data and axes don't overlap.
fill	The fill color of the boxes. The default is to use the color column included in dat. If a custom dataset is provided with dat without a color column and without fill, a greyscale will be used. Custom fill colors can be provided with this option (overriding the color column) 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.
lab	Whether to include labels.
lab_color	The color of the labels. The default is to use the lab_color column included in dat. If a custom dataset is provided with dat without a lab_color column and without fill, all labels will be black. Custom label colors can be provided with this option (overriding the lab_color column) and will be recycled if/as necessary.
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. If abbrv is TRUE, this can also include interval abbreviations.
size	Label size. Either a number as you would specify in ggplot2::geom_text() or "auto" to use ggfittext::geom_fit_text().
lwd	Line width.
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?
dat_is_discrete	Are the ages in dat already converted for a discrete scale?
fittext_args	A list of named arguments to provide to ggfittext::geom_fit_text(). Only used if size is set to "auto".

Details

Transforming the side with the scale is not currently implemented. If a custom data.frame 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 color for the background for each time interval.

• The lab_color column is also optional and lists a color for the label for each time interval.

If the axis of the time scale is discrete, max_age and min_age will automatically be converted to the discrete scale. In this case, the categories of the discrete axis should match the values in the name column. If the ages within dat are already discretized, you can set dat_is_discrete to TRUE to prevent this automatic conversion. This can be useful for adding a time scale where categories and time intervals are not 1:1.

pos may also be a list of sides (including duplicates) if multiple time scales should be added to the plot. In this case, dat, fill, color, alpha, height, lab, lab_color, rot, abbrv, skip, size, lwd, neg, bord, center_end_labels, and dat_is_discrete can also be lists. If these lists are not as long as pos, the elements will be recycled. If individual values (or vectors) are used for these parameters, they will be applied to all time scales (and recycled as necessary).

Examples

library(ggplot2)
# single scale on bottom
ggplot() +
  geom_point(aes(y = runif(1000, 0, 8), x = runif(1000, 0, 1000))) +
  scale_x_reverse() +
  coord_geo(xlim = c(1000, 0), ylim = c(0, 8)) +
  theme_classic()

# stack multiple scales
ggplot() +
  geom_point(aes(y = runif(1000, 0, 8), x = runif(1000, 0, 100))) +
  scale_x_reverse() +
  coord_geo(
    xlim = c(100, 0), ylim = c(0, 8), pos = as.list(rep("bottom", 3)),
    dat = list("stages", "epochs", "periods"),
    height = list(unit(4, "lines"), unit(4, "lines"), unit(2, "line")),
    rot = list(90, 90, 0), size = list(2.5, 2.5, 5), abbrv = FALSE
  ) +
  theme_classic()

deeptime documentation built on Feb. 16, 2023, 10:59 p.m.