facet_abundanceh: Facet for relative abundance data

In paleolimbot/agedepth: Tidy Tools for Paleoenvironmental Archives

Facet for relative abundance data

Description

Provides a number of modifications to the plot that are necessary for relative abundance plots of a number of species. See scale_x_abundance, facet_grid, facet_grid, label_species, label_geochem, and rotated_facet_labels rotated_axis_labels for examples of how to customize the default behaviour.

Usage

facet_abundanceh(
  taxon,
  grouping = NULL,
  rotate_facet_labels = 45,
  labeller = label_species,
  scales = "free_x",
  space = "free_x",
  dont_italicize = c("\\(.*?\\)", "spp?\\.", "-complex", "[Oo]ther"),
  ...
)

facet_abundance(
  taxon,
  grouping = NULL,
  rotate_facet_labels = 0,
  labeller = label_species,
  scales = "free_y",
  space = "free_y",
  dont_italicize = c("\\(.*?\\)", "spp?\\.", "-complex", "[Oo]ther"),
  ...
)

facet_geochem_wraph(
  param,
  grouping = NULL,
  rotate_axis_labels = 90,
  scales = "free_x",
  labeller = label_geochem,
  renamers = c(`^d([0-9]+)([HCNOS])$` = "paste(delta ^ \\1, \\2)", `^210Pb$` =
    "paste({}^210, Pb)", `^Pb210$` = "paste({}^210, Pb)"),
  units = character(0),
  default_units = NA_character_,
  ...
)

facet_geochem_wrap(
  param,
  grouping = NULL,
  scales = "free_y",
  labeller = label_geochem,
  renamers = c(`^d([0-9]+)([HCNOS])$` = "paste(delta ^ \\1, \\2)", `^210Pb$` =
    "paste({}^210, Pb)", `^Pb210$` = "paste({}^210, Pb)"),
  units = character(0),
  default_units = NA_character_,
  ...
)

facet_geochem_grid(
  param,
  grouping = NULL,
  rotate_axis_labels = 0,
  scales = "free_y",
  space = "fixed",
  labeller = label_geochem,
  renamers = c(`^d([0-9]+)([HCNOS])$` = "paste(delta ^ \\1, \\2)", `^210Pb$` =
    "paste({}^210, Pb)", `^Pb210$` = "paste({}^210, Pb)"),
  units = character(0),
  default_units = NA_character_,
  ...
)

facet_geochem_gridh(
  param,
  grouping = NULL,
  rotate_axis_labels = 90,
  scales = "free_x",
  space = "fixed",
  labeller = label_geochem,
  renamers = c(`^d([0-9]+)([HCNOS])$` = "paste(delta ^ \\1, \\2)", `^210Pb$` =
    "paste({}^210, Pb)", `^Pb210$` = "paste({}^210, Pb)"),
  units = character(0),
  default_units = NA_character_,
  ...
)

Arguments

taxon, param	A call to vars, defining the column that identifies the taxon (parameter).
grouping	A call to vars, identifying additional grouping columns
rotate_facet_labels, rotate_axis_labels	Facet (axis) label rotation (degrees)
labeller	Labeller to process facet names. Use label_species to italicize species names, label_geochem to perform common formatting and units, or label_value to suppress.
space, scales	Modify default scale freedom behaviour
dont_italicize	Regular expressions that should not be italicized
...	Passed to facet_grid (abundance) or facet_wrap (geochem).
renamers	Search and replace operations to perform in the form search = replace. Replace text can (should) contain backreferences, and will be parsed as an expression (see plotmath). Use NULL to suppress renaming.
units	A named list of values = unit
default_units	The default units to apply

Value

A subclass of ggplot2::facet_grid() or ggplot2::facet_wrap().

Examples

library(ggplot2)

ggplot(keji_lakes_plottable, aes(x = rel_abund, y = depth)) +
  geom_col_segsh() +
  scale_y_reverse() +
  facet_abundanceh(vars(taxon), grouping = vars(location)) +
  labs(y = "Depth (cm)")

ggplot(keji_lakes_plottable, aes(y = rel_abund, x = depth)) +
  geom_col_segs() +
  scale_x_reverse() +
  facet_abundance(vars(taxon), grouping = vars(location)) +
  labs(x = "Depth (cm)")

ggplot(alta_lake_geochem, aes(x = value, y = depth)) +
  geom_lineh() +
  geom_point() +
  scale_y_reverse() +
  facet_geochem_wrap(vars(param), units = c(C = "%", Cu = "ppm", Ti = "ppm"), nrow = 1) +
  labs(x = NULL, y = "Depth (cm)")

ggplot(alta_lake_geochem, aes(x = value, y = depth)) +
  geom_lineh() +
  geom_point() +
  scale_y_reverse() +
  facet_geochem_gridh(vars(param), units = c(C = "%", Cu = "ppm", Ti = "ppm")) +
  labs(x = NULL, y = "Depth (cm)")

ggplot(alta_lake_geochem, aes(y = value, x = depth)) +
  geom_line() +
  geom_point() +
  scale_x_reverse() +
  facet_geochem_grid(vars(param), units = c(C = "%", Cu = "ppm", Ti = "ppm")) +
  labs(y = NULL, x = "Depth (cm)")

paleolimbot/agedepth documentation built on Feb. 6, 2023, 9:21 p.m.