Title: Plotting Tools for Anyone Working in Deep Time
Version: 2.2.0
Maintainer: William Gearty <willgearty@gmail.com>
Description: Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.
URL: https://williamgearty.com/deeptime/, https://github.com/willgearty/deeptime
BugReports: https://github.com/willgearty/deeptime/issues
Depends: R (≥ 3.5)
License: GPL (≥ 3)
Encoding: UTF-8
RoxygenNote: 7.3.2
LazyData: true
Imports: deeptimedata, ggplot2 (≥ 3.5.0), utils, ggforce, grid, gridExtra, gtable, methods, stats, lattice, rlang (≥ 1.1.0), scales, ggfittext, curl, cli, lifecycle, grImport2, ggh4x
Suggests: geomtextpath, phytools, dplyr, divDyn, gsloid, ape, palaeoverse, paleotree, dispRity, ggtree (≥ 3.6.1), testthat (≥ 3.0.0), vdiffr (≥ 1.0.8), knitr, rmarkdown, withr, ggpattern, ggrepel, rmacrostrat, svglite
VignetteBuilder: knitr
Config/testthat/edition: 3
Config/Needs/revdeps: revdepcheck
NeedsCompilation: no
Packaged: 2025-06-18 21:59:18 UTC; willg
Author: William Gearty ORCID iD [aut, cre]
Repository: CRAN
Date/Publication: 2025-06-19 19:10:07 UTC

deeptime: Plotting Tools for Anyone Working in Deep Time

Description

logo

Extends the functionality of other plotting packages (notably 'ggplot2') to help facilitate the plotting of data over long time intervals, including, but not limited to, geological, evolutionary, and ecological data. The primary goal of 'deeptime' is to enable users to add highly customizable timescales to their visualizations. Other functions are also included to assist with other areas of deep time visualization.

Author(s)

Maintainer: William Gearty willgearty@gmail.com (ORCID)

See Also

Useful links:

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,
  alpha = 1,
  height = unit(2, "line"),
  bord = c("left", "right", "top", "bottom"),
  lwd = 0.25,
  color = "black",
  lab = TRUE,
  lab_color = NULL,
  rot = 0,
  family = "sans",
  fontface = "plain",
  size = 5,
  skip = c("Quaternary", "Holocene", "Late Pleistocene"),
  abbrv = TRUE,
  neg = FALSE,
  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? A setting of "on" (the default) means yes, and a setting of "off" means no. In most cases, the default of "on" should not be changed, as setting clip = "off" can cause unexpected results. It allows drawing of data points anywhere on the plot, including in the plot margins. If limits are set via xlim and ylim and some data points fall outside those limits, then those data points may show up in places such as the axes, the legend, the plot title, or the plot margins.

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.

alpha

The transparency of the fill colors.

height

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

bord

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

lwd

Line width.

color

The outline color of the interval boxes.

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).

family

The font family to use for the labels. There are only three fonts that are guaranteed to work everywhere: “sans” (the default), “serif”, or “mono”.

fontface

The font face to use for the labels. The standard options are "plain" (default), "bold", "italic", and "bold.italic".

size

Label size. Either a number as you would specify in ggplot2::geom_text() or "auto" to use ggfittext::geom_fit_text().

skip

A vector of interval names indicating which intervals should not be labeled. If abbrv is TRUE, this can also include interval abbreviations.

abbrv

If including labels, should the labels be abbreviated? If TRUE, the abbr column will be used for the labels. If FALSE, the name column will be used for the labels. If "auto", the abbreviate() function will be used to abbreviate the values in the name column. Note that the built-in data and data retrieved via get_scale_data() already have built-in abbreviations. However, using the "auto" option here will create new unique abbreviations based on only the intervals that are being plotted. In many cases, this may result in abbreviations that are shorter in length because there are fewer similar interval names to abbreviate.

neg

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

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.

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, alpha, height, bord, lwd, color, lab, lab_color, rot, family, fontface, size, skip, abbrv, neg, 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()

Polar coordinate system with geological timescale

Description

[Deprecated]

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.

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 = -0.5). 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")

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).

Usage

coord_geo_radial(
  dat = "periods",
  theta = "y",
  start = -0.5 * pi,
  end = 1.25 * pi,
  expand = TRUE,
  direction = 1,
  reverse = "none",
  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 to the limits to prevent overlap between data and axes. If FALSE, limits are taken directly from the scale.

direction

1, clockwise; -1, anticlockwise

reverse

A string giving which directions to reverse. "none" (default) keep directions as is. "theta" reverses the angle and "r" reverses the radius. "thetar" reverses both the angle and the radius.

r_axis_inside, rotate_angle

[Deprecated]

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. 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).

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().

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.

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()

Transformed and flipped Cartesian coordinate system

Description

coord_trans_flip 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 flips the x and y coordinates like ggplot2::coord_flip().

Usage

coord_trans_flip(
  x = "identity",
  y = "identity",
  xlim = NULL,
  ylim = NULL,
  clip = "on",
  expand = TRUE
)

Arguments

x, y

Transformers for x and y axes or their names.

xlim, ylim

Limits for the x and y axes.

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. In most cases, the default of "on" should not be changed, as setting clip = "off" can cause unexpected results. It allows drawing of data points anywhere on the plot, including in the plot margins. If limits are set via xlim and ylim and some data points fall outside those limits, then those data points may show up in places such as the axes, the legend, the plot title, or the plot margins.

expand

If TRUE, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If FALSE, limits are taken exactly from the data or xlim/ylim. Giving a logical vector will separately control the expansion for the four directions (top, left, bottom and right). The expand argument will be recycled to length 4 if necessary. Alternatively, can be a named logical vector to control a single direction, e.g. expand = c(bottom = FALSE).

Examples

library(ggplot2)
ggplot(mtcars, aes(disp, wt)) +
  geom_point() +
  coord_trans_flip(x = "log10", y = "log10")

Transformed XY Cartesian coordinate system

Description

coord_trans_xy 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 takes a single transformer that is applied to the x and y axes simultaneously. Any transformers produced by ggforce::linear_trans() that have x and y arguments should work, but any other transformers produced using scales::trans_new() that take x and y arguments should also work. Axis limits will be adjusted to account for transformation unless limits are specified with xlim or ylim.

Usage

coord_trans_xy(
  trans = NULL,
  xlim = NULL,
  ylim = NULL,
  expand = FALSE,
  default = FALSE,
  clip = "on"
)

Arguments

trans

Transformer for x and y axes.

xlim, ylim

Limits for the x and y axes.

expand

If TRUE, the default, adds a small expansion factor to the limits to ensure that data and axes don't overlap. If FALSE, limits are taken exactly from the data or xlim/ylim. Giving a logical vector will separately control the expansion for the four directions (top, left, bottom and right). The expand argument will be recycled to length 4 if necessary. Alternatively, can be a named logical vector to control a single direction, e.g. expand = c(bottom = FALSE).

default

Is this the default coordinate system? If FALSE (the default), then replacing this coordinate system with another one creates a message alerting the user that the coordinate system is being replaced. If TRUE, that warning is suppressed.

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. In most cases, the default of "on" should not be changed, as setting clip = "off" can cause unexpected results. It allows drawing of data points anywhere on the plot, including in the plot margins. If limits are set via xlim and ylim and some data points fall outside those limits, then those data points may show up in places such as the axes, the legend, the plot title, or the plot margins.

Details

This coordinate system only works with geoms where all points are defined with x and y coordinates (e.g., ggplot2::geom_point(), ggplot2::geom_polygon()). This does not currently work with geoms where point coordinates are extrapolated (e.g., ggplot2::geom_rect()). Furthermore, when used with ggplot2 3.5.0 and later, some transformation edge cases may cause problems with rendering axis lines. This includes not currently support "capping" axes. I hope to support all of these geoms, edge cases, and features in the future.

Examples

# make transformer
library(ggforce)
trans <- linear_trans(shear(2, 0), rotate(-pi / 3))

# set up data to be plotted
square <- data.frame(x = c(0, 0, 4, 4), y = c(0, 1, 1, 0))
points <- data.frame(x = runif(100, 0, 4), y = runif(100, 0, 1))

# plot data normally
library(ggplot2)
ggplot(data = points, aes(x = x, y = y)) +
  geom_polygon(data = square, fill = NA, color = "black") +
  geom_point(color = "black") +
  coord_cartesian(expand = FALSE) +
  theme_classic()

# plot data with transformation
ggplot(data = points, aes(x = x, y = y)) +
  geom_polygon(data = square, fill = NA, color = "black") +
  geom_point(color = "black") +
  coord_trans_xy(trans = trans, expand = FALSE) +
  theme_classic()

Disparity through time plot using lattice

Description

Plots points on 2-D surfaces within a a 3-D framework. See lattice::wireframe() and lattice::panel.cloud() for customization options.

Usage

disparity_through_time(
  x,
  data,
  groups,
  pch = 16,
  col.point = c("blue"),
  scales = list(arrows = FALSE, distance = 1, col = "black", z = list(rot = 90)),
  colorkey = FALSE,
  screen = list(z = 90, x = 70, y = 180),
  aspect = c(1.5, 4),
  drape = TRUE,
  col.regions = c("white"),
  alpha.regions = c(1),
  perspective = FALSE,
  R.mat = matrix(c(1, 1, 0, 0, 0, 1, 0, 0, 0, 0, 1, 0, 0, 0, 0, 1), 4, 4),
  par.settings = list(axis.line = list(col = "transparent"), layout.heights =
    list(top.padding = 0, main.key.padding = 0, key.axis.padding = 0, axis.xlab.padding =
    0, xlab.key.padding = 0, key.sub.padding = 0, bottom.padding = 0), layout.widths =
    list(left.padding = 0, key.ylab.padding = 0, ylab.axis.padding = 0, axis.key.padding
    = 0, right.padding = 0)),
  lattice.options = list(axis.padding = list(factor = 0)),
  ...
)

Arguments

x

a formula (most likely of the form z ~ x * y)

data

a data frame in which variables in the formula are to be evaluated

groups

a variable in data to be used as a grouping variable (this is probably the z variable)

pch

the point type

col.point

color(s) for points on surfaces

scales

a list specifying how the axes are drawn (see lattice::xyplot() for details)

colorkey

logical, should a legend be drawn (or a list describing the legend; see lattice::levelplot() for details)

screen

a list of the rotations that should be applied to each axis

aspect

a numeric vector of length 2, giving the relative aspects of the y-size/x-size and z-size/x-size of the enclosing cube

drape

logical, whether the surfaces should be colored based on col.regions and alpha.regions

col.regions

color(s) for surfaces

alpha.regions

alpha value(s) for surfaces

perspective

logical, whether to plot a perspective view

R.mat

a transformational matrix that is applied to the orientation of the axes

par.settings

plotting settings (see lattice::trellis.par.set())

lattice.options

lattice settings (see lattice::lattice.options())

...

Other arguments passed to lattice::wireframe()

Value

An object of class "trellis", as output by lattice::wireframe().

Examples

g <- data.frame(
  x = runif(100, 0, 60), y = runif(100, 0, 10),
  z = factor(rep(periods$name[1:5], each = 20),
    levels = periods$name[1:5]
  )
)
disparity_through_time(z ~ x * y,
  data = g, groups = z, aspect = c(1.5, 2),
  xlim = c(0, 60), ylim = c(0, 10), col.regions = "lightgreen",
  col.point = c("red", "blue")
)

Eon data from the International Commission on Stratigraphy (v2024/12)

Description

A dataset containing the boundary ages, abbreviations, and colors for the eons of the Geologic Time Scale. Based on The ICS International Chronostratigraphic Chart (v2024/12), by Cohen, Finney, Gibbard, and Fan.

Usage

eons

Format

A data frame with 3 rows and 5 variables:

name

eon name

max_age

maximum age, in millions of years

min_age

minimum age, in millions of years

abbr

eon name abbreviations

color

the colors for each eon, according to the Commission for the Geological Map of the World

lab_color

the label colors for each eon, either white or black, whichever has better contrast with the background color, based on recommendations by the International Telecommunication Union

Source

https://stratigraphy.org via https://macrostrat.org/api/v2/defs/intervals?timescale=international%20eons

See Also

Other built-in timescales: epochs, eras, periods, stages

Epoch data from the International Commission on Stratigraphy (v2024/12)

Description

A dataset containing the boundary ages, abbreviations, and colors for the epochs of the Geologic Time Scale. Based on The ICS International Chronostratigraphic Chart (v2024/12), by Cohen, Finney, Gibbard, and Fan.

Usage

epochs

Format

A data frame with 34 rows and 5 variables:

name

epoch name

max_age

maximum age, in millions of years

min_age

minimum age, in millions of years

abbr

epoch name abbreviations

color

the colors for each epoch, according to the Commission for the Geological Map of the World

lab_color

the label colors for each epoch, either white or black, whichever has better contrast with the background color, based on recommendations by the International Telecommunication Union

Source

https://stratigraphy.org via https://macrostrat.org/api/v2/defs/intervals?timescale=international%20epochs

See Also

Other built-in timescales: eons, eras, periods, stages

Era data from the International Commission on Stratigraphy (v2024/12)

Description

A dataset containing the boundary ages, abbreviations, and colors for the eras of the Geologic Time Scale. Based on The ICS International Chronostratigraphic Chart (v2024/12), by Cohen, Finney, Gibbard, and Fan.

Usage

eras

Format

A data frame with 10 rows and 5 variables:

name

era name

max_age

maximum age, in millions of years

min_age

minimum age, in millions of years

abbr

era name abbreviations

color

the colors for each era, according to the Commission for the Geological Map of the World

lab_color

the label colors for each era, either white or black, whichever has better contrast with the background color, based on recommendations by the International Telecommunication Union

Source

https://stratigraphy.org via https://macrostrat.org/api/v2/defs/intervals?timescale=international%20eras

See Also

Other built-in timescales: eons, epochs, periods, stages

Lay out panels in a grid with colored strips

Description

facet_grid_color behaves similarly to ggplot2::facet_grid() in that it forms a matrix of panels defined by row and column faceting variables. The main difference is that it also allows the user to specify the background and label colors of the individual facet strips using the colors and lab_colors arguments. If you have only one variable with many levels, try facet_wrap_color().

Usage

facet_grid_color(
  colors,
  rows = NULL,
  cols = NULL,
  scales = "fixed",
  space = "fixed",
  shrink = TRUE,
  labeller = "label_value",
  lab_colors = "auto",
  as.table = TRUE,
  switch = NULL,
  drop = TRUE,
  margins = FALSE,
  axes = "margins",
  axis.labels = "all"
)

facet_grid_geo(
  colors = stages,
  rows = NULL,
  cols = NULL,
  scales = "fixed",
  space = "fixed",
  shrink = TRUE,
  labeller = "label_value",
  lab_colors = "auto",
  as.table = TRUE,
  switch = NULL,
  drop = TRUE,
  margins = FALSE,
  axes = "margins",
  axis.labels = "all"
)

Arguments

colors

Specifies which colors to use to replace the strip backgrounds. Either A) a function that returns a color for a given strip label, B) the character name of a function that does the same, C) a named character vector with names matching strip labels and values indicating the desired colors, or D) a data.frame representing a lookup table with columns named "name" (matching strip labels) and "color" (indicating desired colors). If the function returns NA, the default background color will be used.

rows, cols

A set of variables or expressions quoted by vars() and defining faceting groups on the rows or columns dimension. The variables can be named (the names are passed to labeller).

For compatibility with the classic interface, rows can also be a formula with the rows (of the tabular display) on the LHS and the columns (of the tabular display) on the RHS; the dot in the formula is used to indicate there should be no faceting on this dimension (either row or column).

scales

Are scales shared across all facets (the default, "fixed"), or do they vary across rows ("free_x"), columns ("free_y"), or both rows and columns ("free")?

space

If "fixed", the default, all panels have the same size. If "free_y" their height will be proportional to the length of the y scale; if "free_x" their width will be proportional to the length of the x scale; or if "free" both height and width will vary. This setting has no effect unless the appropriate scales also vary.

shrink

If TRUE, will shrink scales to fit output of statistics, not raw data. If FALSE, will be range of raw data before statistical summary.

labeller

A function that takes one data frame of labels and returns a list or data frame of character vectors. Each input column corresponds to one factor. Thus there will be more than one with vars(cyl, am). Each output column gets displayed as one separate line in the strip label. This function should inherit from the "labeller" S3 class for compatibility with labeller(). You can use different labeling functions for different kind of labels, for example use label_parsed() for formatting facet labels. label_value() is used by default, check it for more details and pointers to other options.

lab_colors

Specifies which colors to use for the strip labels. Either A) a function that returns a color for a given strip label, B) the character name of a function that does the same, C) a named character vector with names matching strip labels and values indicating the desired colors, D) a data.frame representing a lookup table with columns named "name" (matching strip labels) and "lab_color" (indicating desired colors), or E) "auto" (the default), which set the labels to black or white, whichever has better contrast with the background color, based on recommendations by the International Telecommunication Union. If the function returns NA, the default label color will be used.

as.table

If TRUE, the default, the facets are laid out like a table with highest values at the bottom-right. If FALSE, the facets are laid out like a plot with the highest value at the top-right.

switch

By default, the labels are displayed on the top and right of the plot. If "x", the top labels will be displayed to the bottom. If "y", the right-hand side labels will be displayed to the left. Can also be set to "both".

drop

If TRUE, the default, all factor levels not used in the data will automatically be dropped. If FALSE, all factor levels will be shown, regardless of whether or not they appear in the data.

margins

Either a logical value or a character vector. Margins are additional facets which contain all the data for each of the possible values of the faceting variables. If FALSE, no additional facets are included (the default). If TRUE, margins are included for all faceting variables. If specified as a character vector, it is the names of variables for which margins are to be created.

axes

Determines which axes will be drawn. When "margins" (default), axes will be drawn at the exterior margins. "all_x" and "all_y" will draw the respective axes at the interior panels too, whereas "all" will draw all axes at all panels.

axis.labels

Determines whether to draw labels for interior axes when the axes argument is not "margins". When "all" (default), all interior axes get labels. When "margins", only the exterior axes get labels and the interior axes get none. When "all_x" or "all_y", only draws the labels at the interior axes in the x- or y-direction respectively.

Details

facet_grid_geo(...) is an alias of facet_grid_color() with the default of colors set to stages.

See Also

Other faceting functions: facet_nested_color(), facet_nested_wrap_color(), facet_wrap_color()

Examples

library(ggplot2)
df <- data.frame(x = 1:10, y = 1:10, period = c("Permian", "Triassic"))
ggplot(df) +
  geom_point(aes(x, y)) +
  facet_grid_color(cols = vars(period), colors = periods)

Layout panels in a grid with nested colored strips

Description

facet_nested_color behaves similarly to ggh4x::facet_nested() in that it forms a matrix of panels defined by row and column faceting variables and nests grouped facets. The main difference is that it also allows the user to specify the background and label colors of the individual facet strips using the colors and lab_colors arguments.

Usage

facet_nested_color(
  colors,
  rows = NULL,
  cols = NULL,
  scales = "fixed",
  space = "fixed",
  axes = "margins",
  remove_labels = "none",
  independent = "none",
  shrink = TRUE,
  labeller = "label_value",
  lab_colors = "auto",
  as.table = TRUE,
  switch = NULL,
  drop = TRUE,
  margins = FALSE,
  nest_line = element_line(inherit.blank = TRUE),
  solo_line = FALSE,
  resect = unit(0, "mm"),
  render_empty = TRUE,
  strip = strip_nested(),
  bleed = NULL
)

facet_nested_geo(
  colors = rbind(periods, stages),
  rows = NULL,
  cols = NULL,
  scales = "fixed",
  space = "fixed",
  axes = "margins",
  remove_labels = "none",
  independent = "none",
  shrink = TRUE,
  labeller = "label_value",
  lab_colors = "auto",
  as.table = TRUE,
  switch = NULL,
  drop = TRUE,
  margins = FALSE,
  nest_line = element_line(inherit.blank = TRUE),
  solo_line = FALSE,
  resect = unit(0, "mm"),
  render_empty = TRUE,
  strip = strip_nested(),
  bleed = NULL
)

Arguments

colors

Specifies which colors to use to replace the strip backgrounds. Either A) a function that returns a color for a given strip label, B) the character name of a function that does the same, C) a named character vector with names matching strip labels and values indicating the desired colors, or D) a data.frame representing a lookup table with columns named "name" (matching strip labels) and "color" (indicating desired colors). If the function returns NA, the default background color will be used.

rows, cols

A set of variables or expressions quoted by vars() and defining faceting groups on the rows or columns dimension. The variables can be named (the names are passed to labeller).

For compatibility with the classic interface, rows can also be a formula with the rows (of the tabular display) on the LHS and the columns (of the tabular display) on the RHS; the dot in the formula is used to indicate there should be no faceting on this dimension (either row or column).

scales

A character(1) or logical(1) whether scales are shared across facets or allowed to vary. Interacts with the independent argument. One of the following:

"fixed" or FALSE

Scales are shared across all facets (default).

"free_x"

x-scales are allowed to vary across rows.

"free_y"

y-scales are allowed to vary across columns.

"free" or TRUE

Scales can vary across rows and columns.

space

A character(1) or logical(1) determining whether the size of panels are proportional to the length of the scales. When the independent argument allows for free scales in a dimension, the panel sizes cannot be proportional. Note that the scales argument must be free in the same dimension as the space argument to have an effect.One of the following:

"fixed" or FALSE

All panels have the same size (default).

"free_x"

Panel widths are proportional to the x-scales.

"free_y"

Panel heights are proportional to the y-scales.

"free" or TRUE

Both the widths and heights vary according to scales.

axes

A character(1) or logical(1) where axes should be drawn. One of the following:

"margins" or FALSE

Only draw axes at the outer margins (default).

"x"

Draw axes at the outer margins and all inner x-axes too.

"y"

Draw axes at the outer margins and all inner y-axes too.

"all" or TRUE

Draw the axes for every panel.

remove_labels

A character(1) or logical(1) determining whether axis text is displayed at inner panels. One of the following:

"none" or FALSE

Display axis text at all axes (default).

"x"

Display axis text at outer margins and all inner y-axes.

"y"

Display axis text at outer margins and all inner x-axes.

"all" or TRUE

Only display axis text at the outer margins.

independent

A character(1) or logical(1) determining whether scales can vary within a row or column of panels, like they can be in ggplot2::facet_wrap. The scales argument must be free for the same dimension before they can be set to independent. One of the following:

"none" or FALSE

All y-scales should be fixed in a row and all x-scales are fixed in a column (default).

"x"

x-scales are allowed to vary within a column.

"y"

y-scales are allowed to vary within a row.

"all" or TRUE

Both x- and y-scales are allowed to vary within a column or row respectively.

shrink

If TRUE, will shrink scales to fit output of statistics, not raw data. If FALSE, will be range of raw data before statistical summary.

labeller

A function that takes one data frame of labels and returns a list or data frame of character vectors. Each input column corresponds to one factor. Thus there will be more than one with vars(cyl, am). Each output column gets displayed as one separate line in the strip label. This function should inherit from the "labeller" S3 class for compatibility with labeller(). You can use different labeling functions for different kind of labels, for example use label_parsed() for formatting facet labels. label_value() is used by default, check it for more details and pointers to other options.

lab_colors

Specifies which colors to use for the strip labels. Either A) a function that returns a color for a given strip label, B) the character name of a function that does the same, C) a named character vector with names matching strip labels and values indicating the desired colors, D) a data.frame representing a lookup table with columns named "name" (matching strip labels) and "lab_color" (indicating desired colors), or E) "auto" (the default), which set the labels to black or white, whichever has better contrast with the background color, based on recommendations by the International Telecommunication Union. If the function returns NA, the default label color will be used.

as.table

If TRUE, the default, the facets are laid out like a table with highest values at the bottom-right. If FALSE, the facets are laid out like a plot with the highest value at the top-right.

switch

By default, the labels are displayed on the top and right of the plot. If "x", the top labels will be displayed to the bottom. If "y", the right-hand side labels will be displayed to the left. Can also be set to "both".

drop

If TRUE, the default, all factor levels not used in the data will automatically be dropped. If FALSE, all factor levels will be shown, regardless of whether or not they appear in the data.

margins

Either a logical value or a character vector. Margins are additional facets which contain all the data for each of the possible values of the faceting variables. If FALSE, no additional facets are included (the default). If TRUE, margins are included for all faceting variables. If specified as a character vector, it is the names of variables for which margins are to be created.

nest_line

a theme element, either element_blank() or inheriting from ggplot2::element_line(). Lines are drawn between layers of strips indicating hierarchy. The element inherits from the ggh4x.facet.nestline element in the theme.

solo_line

A logical(1) indicating whether parent strips with a single child should be drawn with a nest_line (TRUE) or the line only applies to parents with multiple children (FALSE, default). Only relevant when nest_line is drawn.

resect

a unit vector of length 1, indicating how much the nesting line should be shortened.

render_empty

A logical(1): whether to draw panels without any data (TRUE, default) or display these as blanks (FALSE).

strip

An object created by a call to a strip function, such as strip_nested().

bleed

[Deprecated] the bleed argument has moved to the strip_nested() function.

Details

facet_nested_geo(...) is an alias of facet_nested_color() with the default of colors set to rbind(periods, stages).

See Also

Other faceting functions: facet_grid_color(), facet_nested_wrap_color(), facet_wrap_color()

Examples

library(ggplot2)
df <- data.frame(x = 1:10, y = 1:10,
                 period = factor(c("Permian", "Triassic", "Jurassic",
                                   "Cretaceous", "Paleogene"),
                                 levels = c("Permian", "Triassic",
                                            "Jurassic", "Cretaceous",
                                            "Paleogene")),
                 era = factor(c("Paleozoic", "Mesozoic", "Mesozoic",
                                "Mesozoic", "Cenozoic"),
                                levels = c("Paleozoic", "Mesozoic",
                                           "Cenozoic")))
ggplot(df, aes(x, y)) +
  geom_point() +
  facet_nested_color(~ era + period, colors = rbind(periods, eras))

Ribbon of panels with nested colored strips

Description

facet_nested_wrap_color behaves similarly to ggh4x::facet_nested_wrap() in that it wraps a sequence of panels onto a two-dimensional layout, and nests grouped facets where possible.. The main difference is that it also allows the user to specify the background and label colors of the individual facet strips using the colors and lab_colors arguments.

Usage

facet_nested_wrap_color(
  facets,
  colors,
  nrow = NULL,
  ncol = NULL,
  scales = "fixed",
  axes = "margins",
  remove_labels = "none",
  shrink = TRUE,
  labeller = "label_value",
  lab_colors = "auto",
  as.table = TRUE,
  drop = TRUE,
  dir = "h",
  strip.position = "top",
  nest_line = element_line(inherit.blank = TRUE),
  solo_line = FALSE,
  resect = unit(0, "mm"),
  trim_blank = TRUE,
  strip = strip_nested(),
  bleed = NULL
)

facet_nested_wrap_geo(
  facets,
  colors = rbind(periods, stages),
  nrow = NULL,
  ncol = NULL,
  scales = "fixed",
  axes = "margins",
  remove_labels = "none",
  shrink = TRUE,
  labeller = "label_value",
  lab_colors = "auto",
  as.table = TRUE,
  drop = TRUE,
  dir = "h",
  strip.position = "top",
  nest_line = element_line(inherit.blank = TRUE),
  solo_line = FALSE,
  resect = unit(0, "mm"),
  trim_blank = TRUE,
  strip = strip_nested(),
  bleed = NULL
)

Arguments

facets

A set of variables or expressions quoted by vars() and defining faceting groups on the rows or columns dimension. The variables can be named (the names are passed to labeller).

For compatibility with the classic interface, can also be a formula or character vector. Use either a one sided formula, ~a + b, or a character vector, c("a", "b").

colors

Specifies which colors to use to replace the strip backgrounds. Either A) a function that returns a color for a given strip label, B) the character name of a function that does the same, C) a named character vector with names matching strip labels and values indicating the desired colors, or D) a data.frame representing a lookup table with columns named "name" (matching strip labels) and "color" (indicating desired colors). If the function returns NA, the default background color will be used.

nrow, ncol

Number of rows and columns.

scales

A character(1) or logical(1) whether scales are shared across facets or allowed to vary. One of the following:

"fixed" or FALSE

Scales are shared across all facets (default).

"free_x"

x-scales are allowed to vary.

"free_y"

y-scales are allowed to vary.

"free" or TRUE

Both scales can vary

axes

A character(1) or logical(1) where axes should be drawn. One of the following:

"margins" or FALSE

Only draw axes at the outer margins (default).

"x"

Draw axes at the outer margins and all inner x-axes too.

"y"

Draw axes at the outer margins and all inner y-axes too.

"all" or TRUE

Draw the axes for every panel.

remove_labels

A character(1) or logical(1) determining whether axis text is displayed at inner panels. One of the following:

"none" or FALSE

Display axis text at all axes (default).

"x"

Display axis text at outer margins and all inner y-axes.

"y"

Display axis text at outer margins and all inner x-axes.

"all" or TRUE

Only display axis text at the outer margins.

shrink

If TRUE, will shrink scales to fit output of statistics, not raw data. If FALSE, will be range of raw data before statistical summary.

labeller

A function that takes one data frame of labels and returns a list or data frame of character vectors. Each input column corresponds to one factor. Thus there will be more than one with vars(cyl, am). Each output column gets displayed as one separate line in the strip label. This function should inherit from the "labeller" S3 class for compatibility with labeller(). You can use different labeling functions for different kind of labels, for example use label_parsed() for formatting facet labels. label_value() is used by default, check it for more details and pointers to other options.

lab_colors

Specifies which colors to use for the strip labels. Either A) a function that returns a color for a given strip label, B) the character name of a function that does the same, C) a named character vector with names matching strip labels and values indicating the desired colors, D) a data.frame representing a lookup table with columns named "name" (matching strip labels) and "lab_color" (indicating desired colors), or E) "auto" (the default), which set the labels to black or white, whichever has better contrast with the background color, based on recommendations by the International Telecommunication Union. If the function returns NA, the default label color will be used.

as.table

If TRUE, the default, the facets are laid out like a table with highest values at the bottom-right. If FALSE, the facets are laid out like a plot with the highest value at the top-right.

drop

If TRUE, the default, all factor levels not used in the data will automatically be dropped. If FALSE, all factor levels will be shown, regardless of whether or not they appear in the data.

dir

Direction: either "h" for horizontal, the default, or "v", for vertical.

strip.position

By default, the labels are displayed on the top of the plot. Using strip.position it is possible to place the labels on either of the four sides by setting strip.position = c("top", "bottom", "left", "right")

nest_line

a theme element, either element_blank() or inheriting from ggplot2::element_line(). Lines are drawn between layers of strips indicating hierarchy. The element inherits from the ggh4x.facet.nestline element in the theme.

solo_line

A logical(1) indicating whether parent strips with a single child should be drawn with a nest_line (TRUE) or the line only applies to parents with multiple children (FALSE, default). Only relevant when nest_line is drawn.

resect

a unit vector of length 1, indicating how much the nesting line should be shortened.

trim_blank

A logical(1). When TRUE (default), does not draw rows and columns containing no panels. When FALSE, the nrow and ncol arguments are taken literally, even when there are more than needed to fit all panels.

strip

An object created by a call to a strip function, such as strip_nested().

bleed

[Deprecated] the bleed argument has moved to the strip_nested() function.

Details

facet_nested_wrap_geo(...) is an alias of facet_nested_wrap_color() with the default of colors set to rbind(periods, stages).

See Also

Other faceting functions: facet_grid_color(), facet_nested_color(), facet_wrap_color()

Examples

library(ggplot2)
df <- data.frame(x = 1:10, y = 1:10,
                 period = factor(c("Permian", "Triassic", "Jurassic",
                                   "Cretaceous", "Paleogene"),
                                 levels = c("Permian", "Triassic",
                                            "Jurassic", "Cretaceous",
                                            "Paleogene")),
                 era = factor(c("Paleozoic", "Mesozoic", "Mesozoic",
                                "Mesozoic", "Cenozoic"),
                                levels = c("Paleozoic", "Mesozoic",
                                           "Cenozoic")))
ggplot(df, aes(x, y)) +
  geom_point() +
  facet_nested_wrap_color(~ era + period, colors = rbind(periods, eras))

Wrap a 1d ribbon of panels into 2d with colored strips

Description

facet_wrap_color behaves similarly to ggplot2::facet_wrap() in that it wraps a 1d sequence of panels into 2d. The main difference is that it also allows the user to specify the background and label colors of the individual facet strips using the colors and lab_colors arguments. This is generally a better use of screen space than facet_grid_color() because most displays are roughly rectangular.

Usage

facet_wrap_color(
  facets,
  colors,
  nrow = NULL,
  ncol = NULL,
  scales = "fixed",
  shrink = TRUE,
  labeller = "label_value",
  lab_colors = "auto",
  as.table = TRUE,
  drop = TRUE,
  dir = "h",
  strip.position = "top",
  axes = "margins",
  axis.labels = "all"
)

facet_wrap_geo(
  facets,
  colors = stages,
  nrow = NULL,
  ncol = NULL,
  scales = "fixed",
  shrink = TRUE,
  labeller = "label_value",
  lab_colors = "auto",
  as.table = TRUE,
  drop = TRUE,
  dir = "h",
  strip.position = "top",
  axes = "margins",
  axis.labels = "all"
)

Arguments

facets

A set of variables or expressions quoted by vars() and defining faceting groups on the rows or columns dimension. The variables can be named (the names are passed to labeller).

For compatibility with the classic interface, can also be a formula or character vector. Use either a one sided formula, ~a + b, or a character vector, c("a", "b").

colors

Specifies which colors to use to replace the strip backgrounds. Either A) a function that returns a color for a given strip label, B) the character name of a function that does the same, C) a named character vector with names matching strip labels and values indicating the desired colors, or D) a data.frame representing a lookup table with columns named "name" (matching strip labels) and "color" (indicating desired colors). If the function returns NA, the default background color will be used.

nrow, ncol

Number of rows and columns.

scales

Should scales be fixed ("fixed", the default), free ("free"), or free in one dimension ("free_x", "free_y")?

shrink

If TRUE, will shrink scales to fit output of statistics, not raw data. If FALSE, will be range of raw data before statistical summary.

labeller

A function that takes one data frame of labels and returns a list or data frame of character vectors. Each input column corresponds to one factor. Thus there will be more than one with vars(cyl, am). Each output column gets displayed as one separate line in the strip label. This function should inherit from the "labeller" S3 class for compatibility with labeller(). You can use different labeling functions for different kind of labels, for example use label_parsed() for formatting facet labels. label_value() is used by default, check it for more details and pointers to other options.

lab_colors

Specifies which colors to use for the strip labels. Either A) a function that returns a color for a given strip label, B) the character name of a function that does the same, C) a named character vector with names matching strip labels and values indicating the desired colors, D) a data.frame representing a lookup table with columns named "name" (matching strip labels) and "lab_color" (indicating desired colors), or E) "auto" (the default), which set the labels to black or white, whichever has better contrast with the background color, based on recommendations by the International Telecommunication Union. If the function returns NA, the default label color will be used.

as.table

[Superseded] The as.table argument is now absorbed into the dir argument via the two letter options. If TRUE, the facets are laid out like a table with highest values at the bottom-right. If FALSE, the facets are laid out like a plot with the highest value at the top-right.

drop

If TRUE, the default, all factor levels not used in the data will automatically be dropped. If FALSE, all factor levels will be shown, regardless of whether or not they appear in the data.

dir

Direction: either "h" for horizontal, the default, or "v", for vertical. When "h" or "v" will be combined with as.table to set final layout. Alternatively, a combination of "t" (top) or "b" (bottom) with "l" (left) or "r" (right) to set a layout directly. These two letters give the starting position and the first letter gives the growing direction. For example "rt" will place the first panel in the top-right and starts filling in panels right-to-left.

strip.position

By default, the labels are displayed on the top of the plot. Using strip.position it is possible to place the labels on either of the four sides by setting strip.position = c("top", "bottom", "left", "right")

axes

Determines which axes will be drawn in case of fixed scales. When "margins" (default), axes will be drawn at the exterior margins. "all_x" and "all_y" will draw the respective axes at the interior panels too, whereas "all" will draw all axes at all panels.

axis.labels

Determines whether to draw labels for interior axes when the scale is fixed and the axis argument is not "margins". When "all" (default), all interior axes get labels. When "margins", only the exterior axes get labels, and the interior axes get none. When "all_x" or "all_y", only draws the labels at the interior axes in the x- or y-direction respectively.

Details

facet_wrap_geo(...) is an alias of facet_wrap_color() with the default of colors set to stages.

See Also

Other faceting functions: facet_grid_color(), facet_nested_color(), facet_nested_wrap_color()

Examples

library(ggplot2)
df <- data.frame(x = 1:10, y = 1:10, period = c("Permian", "Triassic"))
ggplot(df) +
  geom_point(aes(x, y)) +
  facet_wrap_color(vars(period), colors = periods)

Get a FGDC geologic plotting pattern

Description

Retrieve a single geologic pattern as defined in the FGDC Digital Cartographic Standard for Geologic Map Symbolization by the U.S. Geological Survey and the Geologic Data Subcommittee (GDS) of the Federal Geographic Data Committee (FGDC).

Usage

geo_pattern(
  code,
  scale = 2,
  col = NULL,
  fill = NULL,
  alpha = NULL,
  bg = "white"
)

geo_grob(code, col = NULL, fill = NULL, alpha = NULL, bg = "white")

Arguments

code

The number corresponding to the pattern to return. Strings and numbers are permitted.

scale

The visual scale of the pattern (higher values mean the pattern is more zoomed in).

col

The color to use for the lines of the pattern.

fill

The color used to fill various closed shapes (e.g., circles) in the pattern.

alpha

The transparency to use for the fill of the pattern.

bg

The background color to use for the pattern.

Details

For specific codes, see the "pattern numbers" in the full pattern chart for valid code values. Daven Quinn has also assembled more accessible documentation of the map patterns/codes and lithology patterns/codes. rmacrostrat::def_lithologies() can also be used to look up pattern codes for various lithologies (see the "fill" column). Note that codes associated with color variants (e.g., "101-M") are supported but will result in the default color variant instead (usually black and white, e.g., "101-K").

These patterns were originally processed and optimized by Daven Quinn and are hosted on GitHub.

Value

geo_grob() returns a grob object with a single instance of the desired pattern. geo_pattern() returns a GridPattern object with a repeated instance of the desired pattern.

See Also

FGDC patterns: grid.pattern_geo(), scale_fill_geopattern()

Examples

library(grid)
# Get a generic igneous pattern
pattern1 <- geo_pattern(code = "313-K")
# Get the pattern for a sandstone
pattern2 <- geo_pattern(code = "607")

# plot the two patterns
grid.newpage()
grid.draw(rectGrob(gp = gpar(fill = pattern1)))
grid.newpage()
grid.draw(rectGrob(gp = gpar(fill = pattern2)))

Plot a 2-D phylomorphospace in ggplot2

Description

This behaves similar to phytools::phylomorphospace(), but is for plotting a 2-D phylomorphospace with ggplot2::ggplot(). This function works like any other ggplot2 geom; it can be combined with other geoms (see the example below), and the output can be modified using scales, themes, etc.

Usage

geom_phylomorpho(
  tree,
  mapping = NULL,
  data = NULL,
  position = "identity",
  ...,
  seg_args = list(),
  point_args = list(),
  arrow = NULL,
  arrow.fill = NULL,
  lineend = "butt",
  linejoin = "round",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

tree

An object of class "phylo".

mapping

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

  • The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

  • A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

...

Other arguments passed on to both ggplot2::geom_segment() and ggplot2::geom_point().

seg_args

A list of arguments passed only to ggplot2::geom_segment().

point_args

A list of arguments passed only to ggplot2::geom_point().

arrow

specification for arrow heads, as created by grid::arrow().

arrow.fill

fill colour to use for the arrow head (if closed). NULL means use colour aesthetic.

lineend

Line end style (round, butt, square).

linejoin

Line join style (round, mitre, bevel).

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

Details

The ancestral states are estimated using phytools::fastAnc(). Note that phytools is not necessarily installed with deeptime, but it is required to use this function. Following the estimation of the ancestral states, the nodes are connected using ggplot2::geom_segment(), while the tips are indicated using ggplot2::geom_point().

The default expectation is that the order of the data is the same order as the tip labels of the tree (tree$tip.label). However, if this is not the case, you can map the optional label aesthetic to a column in the data that contains the tip names (see example below).

Examples

library(ggplot2)

library(ape)
tr <- rtree(10)
dat <- data.frame(
  x = runif(10), y = runif(10), label = tr$tip.label,
  row.names = tr$tip.label
)
ggplot(dat, aes(x = x, y = y, label = label)) +
  geom_phylomorpho(tr) +
  geom_label(size = 5)

Display points and their range

Description

This geom is like ggplot2::geom_pointrange() in that it draws points and lines. However, unlike ggplot2::geom_pointrange(), this geom takes in sets of x-y points and calculates the ranges/intervals based on those. It then plots both the original points and the ranges using ggplot2::geom_linerange(). In cases where not all points are connected (because of grouping due to aesthetics), the background_line argument can be used to add lines that span the entire point range for each x or y category.

Usage

geom_points_range(
  mapping = NULL,
  data = NULL,
  stat = "points_range",
  position = "identity",
  ...,
  na.rm = FALSE,
  orientation = NA,
  background_line = NULL,
  show.legend = NA,
  inherit.aes = TRUE
)

stat_points_range(
  mapping = NULL,
  data = NULL,
  geom = "points_range",
  position = "identity",
  ...,
  na.rm = FALSE,
  orientation = NA,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

stat

The statistical transformation to use on the data for this layer. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used the override the default coupling between geoms and stats. The stat argument accepts the following:

  • A Stat ggproto subclass, for example StatCount.

  • A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

  • The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

  • A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

...

Arguments passed on to both ggplot2::geom_linerange() and ggplot2::geom_point().

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

orientation

The orientation of the layer. The default (NA) automatically determines the orientation from the aesthetic mapping. In the rare event that this fails it can be given explicitly by setting orientation to either "x" or "y". See the Orientation section for more detail.

background_line

A named list of aesthetic values to use for plotted line segments that span the entire y or x range for each x or y category. The default aesthetics will be used for any aesthetics that are not specified in the list. This can be useful if the plotted groups of points don't overlap but you want a continuous line connecting all points for a given x or y category. If NULL (the default), no line segments will be plotted.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

geom

The geometric object to use to display the data for this layer. When using a ⁠stat_*()⁠ function to construct a layer, the geom argument can be used to override the default coupling between stats and geoms. The geom argument accepts the following:

  • A Geom ggproto subclass, for example GeomPoint.

  • A string naming the geom. To give the geom as a string, strip the function name of the geom_ prefix. For example, to use geom_point(), give the geom as "point".

Aesthetics

geom_points_range() understands the following aesthetics (required aesthetics are in bold):

Computed variables

These are calculated by the 'stat' part of layers and can be accessed with delayed evaluation. stat_points_range() provides the following variables, some of which depend on the orientation:

Orientation

This geom treats each axis differently and, thus, can thus have two orientations. Often the orientation is easy to deduce from a combination of the given mappings and the types of positional scales in use. Thus, ggplot2 will by default try to guess which orientation the layer should have. Under rare circumstances, the orientation is ambiguous and guessing may fail. In that case the orientation can be specified directly using the orientation parameter, which can be either "x" or "y". The value gives the axis that the geom should run along, "x" being the default orientation you would expect for the geom.

Examples

library(ggplot2)

library(palaeoverse)
data(tetrapods)
tetrapod_names <- tetrapods$accepted_name[1:50]
beds_sampled <- sample.int(n = 10, size = 50, replace = TRUE)
occdf <- data.frame(taxon = tetrapod_names, bed = beds_sampled)
ggplot(occdf, aes(y = reorder(taxon, bed, min), x = bed)) +
  geom_points_range()

Label nodes on a phylogenetic tree plotted with ggtree

Description

This geom adds labels to all or a subset of the nodes of a phylogenetic tree that has been plotted using ggtree::ggtree(). It is therefore very similar to ggtree::geom_tiplab(), ggtree::geom_tiplab2(), ggtree::geom_nodelab(), and ggtree::geom_nodelab2(). However, unlike those geoms, this geom is intended to work with all coordinate systems, including coord_geo() and coord_geo_radial().

Usage

geom_text_phylo(
  mapping = NULL,
  data = NULL,
  stat = "identity",
  position = "identity",
  ...,
  parse = FALSE,
  nudge_x = 0,
  nudge_y = 0,
  node_type = "tip",
  auto_adjust = TRUE,
  check_overlap = FALSE,
  size.unit = "mm",
  na.rm = FALSE,
  show.legend = NA,
  inherit.aes = TRUE
)

Arguments

mapping

Set of aesthetic mappings created by aes(). If specified and inherit.aes = TRUE (the default), it is combined with the default mapping at the top level of the plot. You must supply mapping if there is no plot mapping.

data

The data to be displayed in this layer. There are three options:

If NULL, the default, the data is inherited from the plot data as specified in the call to ggplot().

A data.frame, or other object, will override the plot data. All objects will be fortified to produce a data frame. See fortify() for which variables will be created.

A function will be called with a single argument, the plot data. The return value must be a data.frame, and will be used as the layer data. A function can be created from a formula (e.g. ~ head(.x, 10)).

stat

The statistical transformation to use on the data for this layer. When using a ⁠geom_*()⁠ function to construct a layer, the stat argument can be used the override the default coupling between geoms and stats. The stat argument accepts the following:

  • A Stat ggproto subclass, for example StatCount.

  • A string naming the stat. To give the stat as a string, strip the function name of the stat_ prefix. For example, to use stat_count(), give the stat as "count".

position

A position adjustment to use on the data for this layer. This can be used in various ways, including to prevent overplotting and improving the display. The position argument accepts the following:

  • The result of calling a position function, such as position_jitter(). This method allows for passing extra arguments to the position.

  • A string naming the position adjustment. To give the position as a string, strip the function name of the position_ prefix. For example, to use position_jitter(), give the position as "jitter".

...

Other arguments passed on to layer()'s params argument. These arguments broadly fall into one of 4 categories below. Notably, further arguments to the position argument, or aesthetics that are required can not be passed through .... Unknown arguments that are not part of the 4 categories below are ignored.

  • Static aesthetics that are not mapped to a scale, but are at a fixed value and apply to the layer as a whole. For example, colour = "red" or linewidth = 3. The geom's documentation has an Aesthetics section that lists the available options. The 'required' aesthetics cannot be passed on to the params. Please note that while passing unmapped aesthetics as vectors is technically possible, the order and required length is not guaranteed to be parallel to the input data.

  • When constructing a layer using a ⁠stat_*()⁠ function, the ... argument can be used to pass on parameters to the geom part of the layer. An example of this is stat_density(geom = "area", outline.type = "both"). The geom's documentation lists which parameters it can accept.

  • Inversely, when constructing a layer using a ⁠geom_*()⁠ function, the ... argument can be used to pass on parameters to the stat part of the layer. An example of this is geom_area(stat = "density", adjust = 0.5). The stat's documentation lists which parameters it can accept.

  • The key_glyph argument of layer() may also be passed on through .... This can be one of the functions described as key glyphs, to change the display of the layer in the legend.

parse

If TRUE, the labels will be parsed into expressions and displayed as described in ?plotmath.

nudge_x, nudge_y

Horizontal and vertical adjustment to nudge labels by. Useful for offsetting text from points, particularly on discrete scales. Cannot be jointly specified with position.

node_type

Determines the subset of nodes to label. Valid options are "tip" for tip nodes, "internal" for non-tip nodes, and "all" for all nodes.

auto_adjust

Should upside-down text labels automatically be rotated 180° to improve readability?

check_overlap

If TRUE, text that overlaps previous text in the same layer will not be plotted. check_overlap happens at draw time and in the order of the data. Therefore data should be arranged by the label column before calling geom_text(). Note that this argument is not supported by geom_label().

size.unit

How the size aesthetic is interpreted: as millimetres ("mm", default), points ("pt"), centimetres ("cm"), inches ("in"), or picas ("pc").

na.rm

If FALSE, the default, missing values are removed with a warning. If TRUE, missing values are silently removed.

show.legend

logical. Should this layer be included in the legends? NA, the default, includes if any aesthetics are mapped. FALSE never includes, and TRUE always includes. It can also be a named logical vector to finely select the aesthetics to display. To include legend keys for all levels, even when no data exists, use TRUE. If NA, all levels are shown in legend, but unobserved levels are omitted.

inherit.aes

If FALSE, overrides the default aesthetics, rather than combining with them. This is most useful for helper functions that define both data and aesthetics and shouldn't inherit behaviour from the default plot specification, e.g. borders().

Details

Each label will be plotted with the same angle as the branch/edge leading to its node by default. The angle, hjust, and vjust aesthetics can be used to adjust this. If custom angle values are specified, these will be added to the default angle as calculated as described above.

As with ggplot2::geom_text(), the limits of axes will not be expanded to accommodate the new labels, so you may need to extend them manually using the limits or expand arguments within scale_ or coord_ functions. Note that coord_geo() by default sets expand = FALSE.

Aesthetics

geom_text_phylo() understands the following aesthetics (required aesthetics are in bold):

Alignment

You can modify text alignment with the vjust and hjust aesthetics. These can either be a number between 0 (left/bottom) and 1 (right/top) or a character ("left", "middle", "right", "bottom", "center", "top"). There are two special alignments: "inward" and "outward". Inward always aligns text towards the center, and outward aligns it away from the center.

Examples

library(ggplot2)

library(ape)
library(ggtree)
tr <- rtree(10)
revts(ggtree(tr)) +
  geom_text_phylo() +
  coord_geo_radial("epochs")

Get geological timescale data

Description

[Deprecated]

getScaleData() was renamed to get_scale_data() as of deeptime version 1.0.0 to create a more consistent API.

Usage

getScaleData(name)

Get geological timescale data

Description

This function takes a name of a geological timescale and returns data for the timescale. Valid names include those of built-in data.frames (periods(), epochs(), stages(), eons(), or eras()), partial matches of those names (e.g., "per" or "age"), and partial or exact matches to those hosted by Macrostrat (see Details below). Note that the colors in the built-in data.frames are according to the Commission for the Geological Map of the World. If you would like to obtain custom Macrostrat colors that are better for mapping, you should specify the full name of a timescale (e.g., "international periods") and set true_colors to FALSE. Note that these colors only vary for the Precambrian.

Usage

get_scale_data(name, true_colors = TRUE)

Arguments

name

The name of the desired timescale.

true_colors

Return original international time scale colors? (as opposed to custom Macrostrat plotting colors)

Details

The following timescales are available from the Macrostrat API as of 2025-06-18:

The most up-to-date list can be found via the Macrostrat API here.

Value

A data.frame with the following columns:

name

the names of the time intervals

max_age

the oldest boundaries of the time intervals, in millions of years

min_age

the youngest boundaries of the time intervals, in millions of years

abbr

either traditional abbreviations of the names of the time intervals (if they exist) or custom abbreviations created with R

color

hex color codes associated with the time intervals (if applicable)

lab_color

default label colors for the time interals, either white or black, whichever has better contrast with the background color, based on recommendations by the International Telecommunication Union

Combine and arrange multiple ggplot-like objects

Description

Arrange multiple ggplot, grobified ggplot, or geo_scale objects on a page, aligning the plot panels, axes, and axis titles.

Usage

ggarrange2(
  ...,
  plots = list(...),
  layout = NULL,
  nrow = NULL,
  ncol = NULL,
  widths = NULL,
  heights = NULL,
  byrow = TRUE,
  top = NULL,
  bottom = NULL,
  left = NULL,
  right = NULL,
  padding = unit(0.5, "line"),
  margin = unit(0.5, "line"),
  clip = "on",
  draw = TRUE,
  newpage = TRUE,
  debug = FALSE,
  labels = NULL,
  label.args = list(gp = gpar(font = 4, cex = 1.2))
)

Arguments

...

ggplot, grobified ggplot (gtable), or geo_scale objects

plots

list of ggplot, gtable, or geo_scale objects

layout

a matrix of integers specifying where each plot should go, like mat in graphics::layout(); NA or a value less than 0 or greater than the number of plots indicates a blank plot; overrides nrow/ncol/byrow

nrow

number of rows

ncol

number of columns

widths

list of requested widths

heights

list of requested heights

byrow

logical, fill by rows

top

optional string, or grob

bottom

optional string, or grob

left

optional string, or grob

right

optional string, or grob

padding

unit of length one, margin around annotations

margin

vector of units of length 4: top, right, bottom, left (as in gtable::gtable_add_padding())

clip

argument of gtable

draw

logical: draw or return a grob

newpage

logical: draw on a new page

debug

logical, show layout with thin lines

labels

character labels used for annotation of subfigures (should be in the same order as plots)

label.args

label list of parameters for the formatting of labels

Value

gtable of aligned plots

Examples

library(ggplot2)
p1 <- ggplot(mtcars, aes(mpg, wt, colour = factor(cyl))) +
  geom_point()
p2 <- ggplot(mtcars, aes(mpg, wt, colour = factor(cyl))) +
  geom_point() +
  facet_wrap(~cyl, ncol = 2, scales = "free") +
  guides(colour = "none") +
  theme()
ggarrange2(p1, p2, widths = c(2, 1), labels = c("a", "b"))

p3 <- 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()
ggarrange2(ggarrange2(p1, p2, widths = c(2, 1), draw = FALSE), p3, nrow = 2)

Add a geologic scale below ggplots using grid

Description

[Deprecated]

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.

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)

Add a geologic scale on top of ggplots

Description

[Deprecated]

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

Usage

gggeo_scale_old(
  gg,
  dat = "periods",
  fill = NULL,
  color = "black",
  alpha = 1,
  height = 0.05,
  gap = 0,
  pos = "bottom",
  lab = TRUE,
  rot = 0,
  abbrv = TRUE,
  skip = c("Quaternary", "Holocene", "Late Pleistocene"),
  size = 5,
  neg = FALSE
)

Arguments

gg

The ggplot object.

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 proportional height (or width if pos is left or right) of the entire plot to use for the scale.

gap

The proportional height (or width) of the entire plot to use as a gap between the axis and 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.

neg

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

Details

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

Value

A ggplot object.

Life cycle

This function is fully deprecated in favor of coord_geo() as of deeptime version 1.2.0. It will be removed in a future version.

Plot an individual FGDC pattern using grid

Description

This function can be used to plot a single geologic pattern as defined in the FGDC Digital Cartographic Standard for Geologic Map Symbolization by the U.S. Geological Survey and the Geologic Data Subcommittee (GDS) of the Federal Geographic Data Committee (FGDC). The pattern is plotted on the existing canvas (i.e., use grid::grid.newpage() to make a new canvas).

Usage

grid.pattern_geo(params, boundary_df, aspect_ratio, legend = FALSE)

Arguments

params

A list of pattern parameters to customize the plotted pattern (see "Details").

boundary_df

A data.frame consisting of three columns: "x" (x-coordinates), "y" (y-coordinates), and "id" (polygon group ID). This data.frame defines the boundary (as a closed polygon) of the plotted pattern.

aspect_ratio

Unused.

legend

Unused.

Details

The following params are accepted:

pattern_alpha

Alpha transparency for pattern. default: 1

pattern_colour

Color used for strokes and points in the pattern. default: 'black'

pattern_fill

Color used to fill various closed shapes (e.g., circles) in the pattern. default: NA

pattern_scale

Scale. default: 2

pattern_type

Code for the FGDC pattern to use. See geo_pattern() for more details. default: "101"

fill

Color used for the background. default: "white"

Warning

Pattern fills are not supported on all graphics devices. Not all devices are under active development, and such devices are unlikely to add support for new features (such as pattern fills). The new features have only been implemented on a subset of graphics devices so far: cairo_pdf(), cairo_ps(), x11(type="cairo"), png(type="cairo"), jpeg(type="cairo"), tiff(type="cairo"), svg(), and pdf(). Although there is no support yet for quartz() or windows(), almost all of the graphics devices above will work on all major platforms. Further, the ragg and svglite packages contain graphics devices that support patterns. When using a graphics device where patterns are not supported, closed shapes will be rendered with a transparent fill. Note that, at least on Windows machines, the default device in RStudio and in the knitr package is png(), which does not support patterns. In RStudio, you can go to ‘Tools > Global Options > General > Graphics’ and choose the ‘Cairo PNG’ device from the dropdown menu to display patterns. Similar issues may arise when using RStudio on other operating systems.

See Also

FGDC patterns: geo_pattern(), scale_fill_geopattern()

Examples

# use the function directly to make a hexagon with the pattern
library(grid)
x <- 0.5 + 0.5 * cos(seq(2 * pi / 4, by = 2 * pi / 6, length.out = 6))
y <- 0.5 + 0.5 * sin(seq(2 * pi / 4, by = 2 * pi / 6, length.out = 6))
grid.newpage()
grid.pattern_geo(params = list(pattern_type = "633", pattern_scale = 4),
                 boundary_df = data.frame(x, y, id = 1))

# use the function via ggpattern by specifying `pattern = 'geo'`
library(ggplot2)
library(ggpattern)
df <- data.frame(trt = c("a", "b", "c"), outcome = c(2.3, 1.9, 3.2))
ggplot(df, aes(trt, outcome)) +
  geom_col_pattern(aes(color = trt, pattern_type = trt), pattern = 'geo',
  pattern_color = "black", fill = "white", pattern_fill = "white") +
  scale_pattern_type_manual(values = c("101", "313", "634")) +
  scale_color_viridis_d() +
  theme(legend.key.size = unit(1.5, 'cm'))

Decompose a ggplot gtable

Description

Reformat the gtable associated with a ggplot object into a 7x7 gtable where the central cell corresponds to the plot panel(s), the rectangle of cells around that corresponds to the axes, and the rectangle of cells around that corresponds to the axis titles.

Usage

gtable_frame2(
  g,
  width = unit(1, "null"),
  height = unit(1, "null"),
  debug = FALSE
)

Arguments

g

gtable

width

requested width

height

requested height

debug

logical draw gtable cells

Value

7x7 gtable wrapping the plot

Examples

library(grid)
library(gridExtra)
library(ggplot2)
p1 <- ggplot(mtcars, aes(mpg, wt, colour = factor(cyl))) +
  geom_point()

p2 <- ggplot(mtcars, aes(mpg, wt, colour = factor(cyl))) +
  geom_point() +
  facet_wrap(~cyl, ncol = 2, scales = "free") +
  guides(colour = "none") +
  theme()

p3 <- ggplot(mtcars, aes(mpg, wt, colour = factor(cyl))) +
  geom_point() +
  facet_grid(. ~ cyl, scales = "free")

g1 <- ggplotGrob(p1)
g2 <- ggplotGrob(p2)
g3 <- ggplotGrob(p3)
fg1 <- gtable_frame2(g1)
fg2 <- gtable_frame2(g2)
fg12 <- gtable_frame2(gtable_rbind(fg1, fg2), width = unit(2, "null"),
                      height = unit(1, "null"))
fg3 <- gtable_frame2(g3, width = unit(1, "null"), height = unit(1, "null"))
grid.newpage()
combined <- gtable_cbind(fg12, fg3)
grid.draw(combined)

Geological timescale axis guide

Description

guide_geo behaves similarly to ggplot2::guide_axis() in that it modifies the visual appearance of the axis. The main difference is that it adds a geological timescale instead of an axis.

Usage

guide_geo(
  dat = "periods",
  fill = NULL,
  alpha = 1,
  height = unit(2, "line"),
  bord = c("left", "right", "top", "bottom"),
  lwd = 0.25,
  color = "black",
  lab = TRUE,
  lab_color = NULL,
  rot = 0,
  family = "sans",
  fontface = "plain",
  size = 5,
  skip = c("Quaternary", "Holocene", "Late Pleistocene"),
  abbrv = TRUE,
  neg = FALSE,
  end_labels = "center",
  dat_is_discrete = FALSE,
  fittext_args = list(),
  theme = NULL,
  title = waiver(),
  order = 0,
  position = waiver()
)

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).

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.

alpha

The transparency of the fill colors.

height

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

bord

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

lwd

Line width.

color

The outline color of the interval boxes.

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).

family

The font family to use for the labels. There are only three fonts that are guaranteed to work everywhere: “sans” (the default), “serif”, or “mono”.

fontface

The font face to use for the labels. The standard options are "plain" (default), "bold", "italic", and "bold.italic".

size

Label size. Either a number as you would specify in ggplot2::geom_text() or "auto" to use ggfittext::geom_fit_text().

skip

A vector of interval names indicating which intervals should not be labeled. If abbrv is TRUE, this can also include interval abbreviations.

abbrv

If including labels, should the labels be abbreviated? If TRUE, the abbr column will be used for the labels. If FALSE, the name column will be used for the labels. If "auto", the abbreviate() function will be used to abbreviate the values in the name column. Note that the built-in data and data retrieved via get_scale_data() already have built-in abbreviations. However, using the "auto" option here will create new unique abbreviations based on only the intervals that are being plotted. In many cases, this may result in abbreviations that are shorter in length because there are fewer similar interval names to abbreviate.

neg

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

end_labels

How should labels for intervals at the ends of the guide be treated? "center", the default, centers the labels within the visible part of the label. "clip" removes the labels if their midpoint is beyond the axis limits. "keep" plots the labels in the midpoint of the full interval.

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".

theme

A theme object to style the guide individually or differently from the plot's theme settings. The theme argument in the guide partially overrides, and is combined with, the plot's theme.

title

A character string or expression indicating a title of guide. If NULL, the title is not shown. By default (waiver()), the name of the scale object or the name specified in labs() is used for the title.

order

A positive integer of length 1 that specifies the order of this guide among multiple guides. This controls in which order guides are merged if there are multiple guides for the same position. If 0 (default), the order is determined by a secret algorithm.

position

Where this guide should be drawn: one of top, bottom, left, or right.

Details

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.

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.

Since this guide only plots the timescale and not ticks or an axis line, a call to this function should almost always be combined with a call to ggplot2::guide_axis() within a call to ggplot2::guide_axis_stack() (see Examples). Note that in most cases this has the same end result as a single call to coord_geo(); however, there are some use cases in which this may be more useful or allow for more customization. For example, users may wish to combine this guide in unique ways with other guides. Further, since coord_geo() doesn't work with radial/fan phylogenies (and coord_geo_radial() is quite different visually), this guide can be used to achieve the look of coord_geo() on a radial/fan phylogeny.

Examples

library(ggplot2)
# reproduce the coord_geo() appearance
ggplot() +
  geom_point(aes(y = runif(1000, 0, 8), x = runif(1000, 0, 1000))) +
  scale_x_reverse(guide = guide_axis_stack(guide_geo(), "axis",
                  spacing = unit(0, "npc"))) +
  coord_cartesian(xlim = c(1000, 0), ylim = c(0, 8)) +
  theme_classic()

# the coord_geo() look on a radial phylogeny
library(ggtree)
library(paleotree)
data(RaiaCopesRule)
ggtree(ceratopsianTreeRaia,
       position = position_nudge(x = -ceratopsianTreeRaia$root.time)) +
  coord_geo_radial(dat = "stages", fill = c("grey80", "grey95"),
                   end = 1.25 * pi) +
  guides(
    r = guide_axis_stack(guide_geo(rot = -90, neg = TRUE,
                                   height = unit(0.5, "line")),
                         "axis", spacing = unit(0, "npc"))
  ) +
  scale_y_continuous(guide = "none", breaks = NULL) +
  theme_classic()

Combined wireframe and cloud panel

Description

Plots the provided data on 2-D surfaces within a 3-D framework. See disparity_through_time().

Usage

panel.disparity(x, y, z, groups, subscripts, ...)

Arguments

x, y, z, groups, subscripts, ...

Same as for lattice::panel.cloud()

Value

No return value, plots the results of both lattice::panel.cloud() and lattice::panel.wireframe().

Period data from the International Commission on Stratigraphy (v2024/12)

Description

A dataset containing the boundary ages, abbreviations, and colors for the periods of the Geologic Time Scale. Based on The ICS International Chronostratigraphic Chart (v2024/12), by Cohen, Finney, Gibbard, and Fan.

Usage

periods

Format

A data frame with 22 rows and 5 variables:

name

period name

max_age

maximum age, in millions of years

min_age

minimum age, in millions of years

abbr

period name abbreviations

color

the colors for each period, according to the Commission for the Geological Map of the World

lab_color

the label colors for each period, either white or black, whichever has better contrast with the background color, based on recommendations by the International Telecommunication Union

Source

https://stratigraphy.org via https://macrostrat.org/api/v2/defs/intervals?timescale=international%20periods

See Also

Other built-in timescales: eons, epochs, eras, stages

Geological Time Scale color scales

Description

Color scales using the colors in the Geological Time Scale graphics.

Usage

scale_color_geo(dat, ...)

scale_fill_geo(dat, ...)

scale_discrete_geo(dat, aesthetics, ...)

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 coord_geo()).

...

Arguments passed on to ggplot2::discrete_scale

scale_name

[Deprecated] The name of the scale that should be used for error messages associated with this scale.

name

The name of the scale. Used as the axis or legend title. If waiver(), the default, the name of the scale is taken from the first mapping used for that aesthetic. If NULL, the legend title will be omitted.

minor_breaks

One of:

  • NULL for no minor breaks

  • waiver() for the default breaks (none for discrete, one minor break between each major break for continuous)

  • A numeric vector of positions

  • A function that given the limits returns a vector of minor breaks. Also accepts rlang lambda function notation. When the function has two arguments, it will be given the limits and major break positions.

labels

One of the options below. Please note that when labels is a vector, it is highly recommended to also set the breaks argument as a vector to protect against unintended mismatches.

  • NULL for no labels

  • waiver() for the default labels computed by the transformation object

  • A character vector giving labels (must be same length as breaks)

  • An expression vector (must be the same length as breaks). See ?plotmath for details.

  • A function that takes the breaks as input and returns labels as output. Also accepts rlang lambda function notation.

limits

One of:

  • NULL to use the default scale values

  • A character vector that defines possible values of the scale and their order

  • A function that accepts the existing (automatic) values and returns new ones. Also accepts rlang lambda function notation.

na.translate

Unlike continuous scales, discrete scales can easily show missing values, and do so by default. If you want to remove missing values from a discrete scale, specify na.translate = FALSE.

na.value

If na.translate = TRUE, what aesthetic value should the missing values be displayed as? Does not apply to position scales where NA is always placed at the far right.

drop

Should unused factor levels be omitted from the scale? The default, TRUE, uses the levels that appear in the data; FALSE includes the levels in the factor. Please note that to display every level in a legend, the layer should use show.legend = TRUE.

guide

A function used to create a guide or its name. See guides() for more information.

call

The call used to construct the scale for reporting messages.

super

The super class to use for the constructed scale

aesthetics

Character string or vector of character strings listing the name(s) of the aesthetic(s) that this scale works with. This can be useful, for example, to apply colour settings to the colour and fill aesthetics at the same time, via aesthetics = c("colour", "fill").

Examples

library(ggplot2)
df <- data.frame(
  x = runif(1000, 0, 10), y = runif(1000, 0, 10),
  color = sample(periods$name, 1000, TRUE), shape = 21
)
ggplot(df) +
  geom_point(aes(x = x, y = y, fill = color), shape = 21) +
  scale_fill_geo("periods", name = "Period") +
  theme_classic()

# cut continuous variable into discrete
df <- data.frame(x = runif(1000, 0, 1000), y = runif(1000, 0, 8))
df$color <- cut(df$x, c(periods$min_age, periods$max_age[22]), periods$name)
ggplot(df) +
  geom_point(aes(x = x, y = y, color = color)) +
  scale_x_reverse() +
  scale_color_geo("periods", name = "Period") +
  coord_geo(xlim = c(1000, 0), ylim = c(0, 8)) +
  theme_classic()

Geologic pattern fill scale

Description

Fill scale using the FGDC Digital Cartographic Standard for Geologic Map Symbolization. Fill values should correspond to specific pattern codes (see "Details").

Usage

scale_fill_geopattern(na.value = "grey50", ...)

Arguments

na.value

The aesthetic value to use for missing (NA) values. May be either a color or a GridPattern object (such as that returned by geo_pattern()).

...

Arguments passed on to ggplot2::discrete_scale

scale_name

[Deprecated] The name of the scale that should be used for error messages associated with this scale.

name

The name of the scale. Used as the axis or legend title. If waiver(), the default, the name of the scale is taken from the first mapping used for that aesthetic. If NULL, the legend title will be omitted.

breaks

One of:

  • NULL for no breaks

  • waiver() for the default breaks (the scale limits)

  • A character vector of breaks

  • A function that takes the limits as input and returns breaks as output. Also accepts rlang lambda function notation.

minor_breaks

One of:

  • NULL for no minor breaks

  • waiver() for the default breaks (none for discrete, one minor break between each major break for continuous)

  • A numeric vector of positions

  • A function that given the limits returns a vector of minor breaks. Also accepts rlang lambda function notation. When the function has two arguments, it will be given the limits and major break positions.

labels

One of the options below. Please note that when labels is a vector, it is highly recommended to also set the breaks argument as a vector to protect against unintended mismatches.

  • NULL for no labels

  • waiver() for the default labels computed by the transformation object

  • A character vector giving labels (must be same length as breaks)

  • An expression vector (must be the same length as breaks). See ?plotmath for details.

  • A function that takes the breaks as input and returns labels as output. Also accepts rlang lambda function notation.

limits

One of:

  • NULL to use the default scale values

  • A character vector that defines possible values of the scale and their order

  • A function that accepts the existing (automatic) values and returns new ones. Also accepts rlang lambda function notation.

na.translate

Unlike continuous scales, discrete scales can easily show missing values, and do so by default. If you want to remove missing values from a discrete scale, specify na.translate = FALSE.

drop

Should unused factor levels be omitted from the scale? The default, TRUE, uses the levels that appear in the data; FALSE includes the levels in the factor. Please note that to display every level in a legend, the layer should use show.legend = TRUE.

guide

A function used to create a guide or its name. See guides() for more information.

call

The call used to construct the scale for reporting messages.

Details

For specific codes, see the "pattern numbers" in the full pattern chart for valid code values. Daven Quinn has also assembled more accessible documentation of the map patterns/codes and lithology patterns/codes. rmacrostrat::def_lithologies() can also be used to look up pattern codes for various lithologies (see the "fill" column). Note that codes associated with color variants (e.g., "101-M") are supported but will result in the default color variant instead (usually black and white, e.g., "101-K").

These patterns were originally processed and optimized by Daven Quinn and are hosted on GitHub.

Warning

Pattern fills are not supported on all graphics devices. Not all devices are under active development, and such devices are unlikely to add support for new features (such as pattern fills). The new features have only been implemented on a subset of graphics devices so far: cairo_pdf(), cairo_ps(), x11(type="cairo"), png(type="cairo"), jpeg(type="cairo"), tiff(type="cairo"), svg(), and pdf(). Although there is no support yet for quartz() or windows(), almost all of the graphics devices above will work on all major platforms. Further, the ragg and svglite packages contain graphics devices that support patterns. When using a graphics device where patterns are not supported, closed shapes will be rendered with a transparent fill. Note that, at least on Windows machines, the default device in RStudio and in the knitr package is png(), which does not support patterns. In RStudio, you can go to ‘Tools > Global Options > General > Graphics’ and choose the ‘Cairo PNG’ device from the dropdown menu to display patterns. Similar issues may arise when using RStudio on other operating systems.

See Also

FGDC patterns: geo_pattern(), grid.pattern_geo()

Examples

library(ggplot2)
vals <- c("101", "313", "603", "733")
ggplot(mpg, aes(factor(cyl), fill = vals[factor(cyl)])) +
  geom_bar() +
  scale_fill_geopattern(name = NULL)

Stage data from the International Commission on Stratigraphy (v2024/12)

Description

A dataset containing the boundary ages, abbreviations, and colors for the stages of the Geologic Time Scale. Based on The ICS International Chronostratigraphic Chart (v2024/12), by Cohen, Finney, Gibbard, and Fan.

Usage

stages

Format

A data frame with 102 rows and 5 variables:

name

stage name

max_age

maximum age, in millions of years

min_age

minimum age, in millions of years

abbr

stage name abbreviations

color

the colors for each stage, according to the Commission for the Geological Map of the World

lab_color

the label colors for each stage, either white or black, whichever has better contrast with the background color, based on recommendations by the International Telecommunication Union

Source

https://stratigraphy.org via https://macrostrat.org/api/v2/defs/intervals?timescale=international%20ages

See Also

Other built-in timescales: eons, epochs, eras, periods