coord_geo_radial: Enhanced polar coordinate system with geological timescale

In willgearty/deeptime: Plotting Tools for Anyone Working in Deep Time

Enhanced polar coordinate system with geological timescale

Description

coord_geo_radial behaves similarly to ggplot2::coord_radial() 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 background of the plot. coord_geo_radial is similar to coord_geo_polar() but has more options related to the polar coordinate plotting that are inherited from ggplot2::coord_radial() (e.g., end, r_axis_inside, inner.radius). Furthermore, unlike coord_geo_polar, coord_geo_radial uses the ggplot2 internals to draw the r and theta axes, gridlines, etc. This means that users can tweak the guide and theme settings for these features (see examples). Note that coord_geo_radial requires ggplot2 v. 3.5.0 or later.

Usage

coord_geo_radial(
  dat = "periods",
  theta = "y",
  start = -0.5 * pi,
  end = 1.25 * pi,
  expand = TRUE,
  direction = 1,
  r_axis_inside = NULL,
  inner.radius = 0.05,
  fill = NULL,
  alpha = 1,
  lwd = 0.25,
  color = "grey80",
  lty = "solid",
  lab = FALSE,
  abbrv = TRUE,
  skip = c("Quaternary", "Holocene", "Late Pleistocene"),
  neg = TRUE,
  prop = 1,
  textpath_args = list(),
  clip = "off",
  rotate_angle = FALSE
)

Arguments

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).
theta	variable to map angle to (x or y)
start	Offset of starting point from 12 o'clock in radians. Offset is applied clockwise or anticlockwise depending on value of direction.
end	Position from 12 o'clock in radians where plot ends, to allow for partial polar coordinates. The default, NULL, is set to start + 2 * pi.
expand	If TRUE, the default, adds a small expansion factor the the limits to prevent overlap between data and axes. If FALSE, limits are taken directly from the scale.
direction	1, clockwise; -1, anticlockwise
r_axis_inside	If TRUE, places the radius axis inside the panel. If FALSE, places the radius axis next to the panel. The default, NULL, places the radius axis outside if the start and end arguments form a full circle.
inner.radius	A numeric between 0 and 1 setting the size of a inner.radius hole.
fill	The fill color of the background. 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.
alpha	The transparency of the fill colors.
lwd	Line width for lines between intervals. Set to NULL to remove lines.
color	The color of the lines between intervals.
lty	Line type for lines between intervals.
lab	Whether to include labels.
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.
neg	Set this to true if your theta-axis is using negative values. This is usually true if you are using ggtree.
prop	This is the rotational proportion of the background that the scale takes up.
textpath_args	A list of named arguments to provide to geomtextpath::geom_textpath(). Only used if lab is set to TRUE. Useful arguments include color (font color), family (font family), fontface, hjust (radial adjustment), and size (font size).
clip	Should drawing be clipped to the extent of the plot panel? A setting of "on" (the default) means yes, and a setting of "off" means no. For details, please see coord_cartesian().
rotate_angle	If TRUE, transforms the angle aesthetic in data in accordance with the computed theta position. If FALSE (default), no such transformation is performed. Can be useful to rotate text geoms in alignment with the coordinates.

Details

If a custom data.frame is provided (with dat), it should consist of at least 2 columns of data. See data(periods) for an example.

• 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 optional and lists a color for the background for each time interval.

dat may also be a list of values and/or dataframes if multiple time scales should be added to the background. Scales will be added sequentially starting at start and going in the specified direction. By default the scales will all be equal in circular/rotational proportion, but this can be overridden with prop. If dat is a list, fill, alpha, lwd, color, lty, lab, abbrv, skip, neg, prop, and textpath_args can also be lists (N.B. textpath_args would be a list of lists). If these lists are not as long as dat, 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).

If the sum of the prop values is greater than 1, the proportions will be scaled such that they sum to 1. However, the prop values may sum to less than 1 if the user would like blank space in the background.

Care must be taken when adding labels to plots, as they are very likely to overlap with the plot under the default settings. The textpath_args argument can be used to adjust the settings for the plotting of the labels. See geomtextpath::geom_textpath() for details about the available arguments. Also note that the curvature of the labels may vary based on the distance from the origin. This is why abbrv is set to TRUE by default.

Examples

library(ggplot2)

library(ggtree)
set.seed(1)
tree <- rtree(100)
# single scale
revts(ggtree(tree)) +
  coord_geo_radial(dat = "stages") +
  scale_y_continuous(guide = "none", breaks = NULL) +
  theme_gray()

# multiple scales
revts(ggtree(tree)) +
  coord_geo_radial(
    dat = list("stages", "periods"), alpha = .5,
    prop = list(0.75, .25), start = pi / 4, end = 2 * pi, lty = "dashed"
  ) +
  scale_y_continuous(expand = expansion(mult = c(0.02, 0.02)),
                     guide = "none", breaks = NULL) +
  theme_gray()


library(ggplot2)
library(paleotree)
data(RaiaCopesRule)
ggtree(ceratopsianTreeRaia,
       position = position_nudge(x = -ceratopsianTreeRaia$root.time)) +
  coord_geo_radial(dat = "stages") +
  scale_y_continuous(guide = "none", breaks = NULL) +
  theme_classic()

willgearty/deeptime documentation built on April 5, 2024, 3:24 a.m.