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

RarefactionPlotAtomic

R Documentation

RarefactionPlotAtomic

Description

This function generates a rarefraction plot for a given dataset.

Usage

RarefactionPlotAtomic(
  data,
  type = 1,
  se = TRUE,
  group_by = "group",
  group_name = NULL,
  pt_size = 3,
  line_width = 1,
  theme = "theme_this",
  theme_args = list(),
  palette = "Spectral",
  palcolor = NULL,
  alpha = 0.2,
  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,
  ...
)

Arguments

`data`	An iNEXT object or a list of data that will be handled by iNEXT::iNEXT.
`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`	A character string indicating how to group the data (color the lines). Possible values are "q" and "group"
`group_name`	A character string indicating the name of the group, showing as the legend title.
`pt_size`	A numeric value specifying the size of the points.
`line_width`	A numeric value specifying the width of the lines.
`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.
`facet_by`	A character string indicating how to facet the data and plots Possible values are "q" and "group"
`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.
`...`	Additional arguments to pass to iNEXT::iNEXT when `data` is not an iNEXT object.