RarefactionPlot — RarefactionPlot • plotthis

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,
  ...
)

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.
...: Additional arguments.

Value

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

Examples

# \donttest{
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)

# }