coord_geo_polar: Polar coordinate system with geological timescale

In deeptime: Plotting Tools for Anyone Working in Deep Time

Polar coordinate system with geological timescale

Description

coord_geo_polar behaves similarly to ggplot2::coord_polar() 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.

Usage

coord_geo_polar(
  dat = "periods",
  theta = "y",
  start = -pi/2,
  direction = -1,
  clip = "on",
  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()
)

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.
direction	1, clockwise; -1, anticlockwise
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().
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. Requires the geomtextpath package.
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).

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.

coord_geo_polar manually generates the r axis, meaning it does not support changing the guide features of ggplot v. 2.5.0 or later. However, the deeptime.axis.line.r, deeptime.axis.text.r, deeptime.axis.ticks.r, and deeptime.axis.ticks.length.r ggplot2 theme elements can be modified just like their x and y counterparts to change the appearance of the radius axis. The default settings work well for a horizontal axis pointing towards the right, but these theme settings will need to be modified for other orientations. The default value for deeptime.axis.line.r is element_line(). The default value for deeptime.axis.text.r is element_text(size = 3.5, vjust = -2, hjust = NA). The default value for deeptime.axis.ticks.r is element_line(). The default value for deeptime.axis.ticks.length.r is unit(1.5, "points"). However, note that the units for this element are meaningless and only the numeric value will be used (but a unit must still be used).

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.

Life cycle

This function is soft-deprecated in favor of coord_geo_radial() as of deeptime version 1.1.0. There is currently no plan to remove this function, but users are strongly encouraged to migrate to the new function for enhanced polar functionality.

Examples

library(ggplot2)

library(ggtree)
set.seed(1)
tree <- rtree(100)
# single scale
revts(ggtree(tree)) +
  coord_geo_polar(dat = "stages")

# multiple scales
revts(ggtree(tree)) +
  coord_geo_polar(
    dat = list("stages", "periods"), alpha = .5,
    prop = list(0.75, .25), start = pi / 4, lty = "dashed"
  ) +
  scale_y_continuous(expand = expansion(mult = c(0.02, 0.02))) +
  theme(deeptime.axis.text.r = element_text(size = 3.5, hjust = .75,
                                            vjust = .75))


library(ggplot2)
library(paleotree)
data(RaiaCopesRule)
ggtree(ceratopsianTreeRaia,
       position = position_nudge(x = -ceratopsianTreeRaia$root.time)) +
  coord_geo_polar(dat = "stages")

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