RarefactionPlot: RarefactionPlot

In plotthis: High-Level Plotting Built Upon 'ggplot2' and Other Plotting Packages

RarefactionPlot

Description

This function generates a rarefraction plot for a given dataset.

Usage

RarefactionPlot(
  data,
  type = 1,
  se = NULL,
  group_by = "group",
  group_by_sep = "_",
  group_name = NULL,
  split_by = NULL,
  split_by_sep = "_",
  theme = "theme_this",
  theme_args = list(),
  palette = "Spectral",
  palcolor = NULL,
  alpha = 0.2,
  pt_size = 3,
  line_width = 1,
  facet_by = NULL,
  facet_scales = "fixed",
  facet_ncol = NULL,
  facet_nrow = NULL,
  facet_byrow = TRUE,
  aspect.ratio = 1,
  legend.position = "right",
  legend.direction = "vertical",
  title = NULL,
  subtitle = NULL,
  xlab = NULL,
  ylab = NULL,
  seed = 8525,
  combine = TRUE,
  nrow = NULL,
  ncol = NULL,
  byrow = TRUE,
  axes = NULL,
  axis_titles = axes,
  guides = NULL,
  design = NULL,
  ...
)

Arguments

data	A data frame.
type	three types of plots: sample-size-based rarefaction/extrapolation curve (type = 1); sample completeness curve (type = 2); coverage-based rarefaction/extrapolation curve (type = 3).
se	a logical variable to display confidence interval around the estimated sampling curve. Default to NULL which means TRUE if the data has the lower and upper bounds.
group_by	Columns to group the data for plotting For those plotting functions that do not support multiple groups, They will be concatenated into one column, using group_by_sep as the separator
group_by_sep	A character string indicating how to separate the group_by column if both "q" and "group" are used. for 'group_by'. Default to "_".
group_name	A character string indicating the name of the group, showing as the legend title.
split_by	A character string indicating how to split the data and plots Possible values are "q" and "group"
split_by_sep	The separator for multiple split_by columns. See split_by
theme	A character string or a theme class (i.e. ggplot2::theme_classic) specifying the theme to use. Default is "theme_this".
theme_args	A list of arguments to pass to the theme function.
palette	A character string specifying the palette to use. A named list or vector can be used to specify the palettes for different split_by values.
palcolor	A character string specifying the color to use in the palette. A named list can be used to specify the colors for different split_by values. If some values are missing, the values from the palette will be used (palcolor will be NULL for those values).
alpha	A numeric value specifying the transparency of the plot.
pt_size	A numeric value specifying the size of the points.
line_width	A numeric value specifying the width of the lines.
facet_by	A character string specifying the column name of the data frame to facet the plot. Otherwise, the data will be split by split_by and generate multiple plots and combine them into one using patchwork::wrap_plots
facet_scales	Whether to scale the axes of facets. Default is "fixed" Other options are "free", "free_x", "free_y". See ggplot2::facet_wrap
facet_ncol	A numeric value specifying the number of columns in the facet. When facet_by is a single column and facet_wrap is used.
facet_nrow	A numeric value specifying the number of rows in the facet. When facet_by is a single column and facet_wrap is used.
facet_byrow	A logical value indicating whether to fill the plots by row. Default is TRUE.
aspect.ratio	A numeric value specifying the aspect ratio of the plot.
legend.position	A character string specifying the position of the legend. if waiver(), for single groups, the legend will be "none", otherwise "right".
legend.direction	A character string specifying the direction of the legend.
title	A character string specifying the title of the plot. A function can be used to generate the title based on the default title. This is useful when split_by is used and the title needs to be dynamic.
subtitle	A character string specifying the subtitle of the plot.
xlab	A character string specifying the x-axis label.
ylab	A character string specifying the y-axis label.
seed	The random seed to use. Default is 8525.
combine	Whether to combine the plots into one when facet is FALSE. Default is TRUE.
nrow	A numeric value specifying the number of rows in the facet.
ncol	A numeric value specifying the number of columns in the facet.
byrow	A logical value indicating whether to fill the plots by row.
axes	A string specifying how axes should be treated. Passed to patchwork::wrap_plots(). Only relevant when split_by is used and combine is TRUE. Options are: 'keep' will retain all axes in individual plots. 'collect' will remove duplicated axes when placed in the same run of rows or columns of the layout. 'collect_x' and 'collect_y' will remove duplicated x-axes in the columns or duplicated y-axes in the rows respectively.
axis_titles	A string specifying how axis titltes should be treated. Passed to patchwork::wrap_plots(). Only relevant when split_by is used and combine is TRUE. Options are: 'keep' will retain all axis titles in individual plots. 'collect' will remove duplicated titles in one direction and merge titles in the opposite direction. 'collect_x' and 'collect_y' control this for x-axis titles and y-axis titles respectively.
guides	A string specifying how guides should be treated in the layout. Passed to patchwork::wrap_plots(). Only relevant when split_by is used and combine is TRUE. Options are: 'collect' will collect guides below to the given nesting level, removing duplicates. 'keep' will stop collection at this level and let guides be placed alongside their plot. 'auto' will allow guides to be collected if a upper level tries, but place them alongside the plot if not.
design	Specification of the location of areas in the layout, passed to patchwork::wrap_plots(). Only relevant when split_by is used and combine is TRUE. When specified, nrow, ncol, and byrow are ignored. See patchwork::wrap_plots() for more details.
...	Additional arguments.

Value

A ggplot object or wrap_plots object or a list of ggplot objects

Examples

set.seed(8525)
spider <- list(
   Girdled = c(46, 22, 17, 15, 15, 9, 8, 6, 6, 4, rep(2, 4), rep(1, 12)),
   Logged = c(88, 22, 16, 15, 13, 10, 8, 8, 7, 7, 7, 5, 4, 4, 4, 3, 3, 3, 3,
     2, 2, 2, 2, rep(1, 14))
)

RarefactionPlot(spider)
RarefactionPlot(spider, q = c(0, 1, 2), facet_by = "q")
RarefactionPlot(spider, q = c(0, 1, 2), split_by = "q")
RarefactionPlot(spider, q = c(0, 1, 2), split_by = "q",
                palette = c("0" = "Paired", "1" = "Set1", "2" = "Dark2"))
RarefactionPlot(spider, q = c(0, 1, 2), group_by = "q",
 facet_by = "group", palette = "Set1", type = 3)

plotthis documentation built on June 8, 2025, 11:11 a.m.