plot_diagram: Plot stratigraphic data as polygons or barplots.

In mchevalier2/crestr: A Probabilistic Approach to Reconstruct Past Climates Using Palaeoecological Datasets

Plot stratigraphic data as polygons or barplots.

Description

This function plots stratigraphic data either as polygons or bars.

Usage

plot_diagram(
  x,
  bars = FALSE,
  col = "black",
  amplif = 5,
  save = FALSE,
  filename = "Diagram.pdf",
  width = 3.54,
  height = 9,
  as.png = FALSE,
  png.res = 300,
  yax_incr = 5,
  bar_width = diff(range(x$inputs$x))/length(x$inputs$x),
  xlim = NA,
  tickAtSample = TRUE,
  col_pos = "black",
  col_neg = "grey80",
  title = NA,
  src = NA
)

Arguments

x	A data frame of the data to plot (first column with age or depth) and the taxa in the following columns. x can also be a crestObj.
bars	A boolean that indicates if the data should be plotted as polygons (default: bars=FALSE) or vertical bars (bars=TRUE).
col	Colours to be used for the polygons. If the number of colours does not match the number of taxa, colors will be recycled.
amplif	A factor the show exaggeration on the diagram. Only for polygon plot. Default 5.
save	A boolean to indicate if the diagram should be saved as a pdf file. Default is FALSE.
filename	An absolute or relative path that indicates where the diagram should be saved. Also used to specify the name of the file. Default: the file is saved in the working directory under the name 'Diagram.pdf'.
width	The width of the output file in inches (default 3.54in ~ 9cm).
height	The height of the output file in inches (default 9in ~ 23cm).
as.png	A boolean to indicate if the output should be saved as a png. Default is FALSE and the figure is saved as a pdf file.
png.res	The resolution of the png file (default 300 pixels per inch).
yax_incr	Graphical parameters describing the increment size on the y-axis (default 5).
bar_width	Width of the bars of the barplot (default 1/50th of the x range).
xlim	The range covered by the x-axis. Can be adjusted to get round numbers on the x-axis. If smaller than the range covered by the data, the data will be truncated (default: range of the data).
tickAtSample	Boolean that indicates whether a tick mark should be added on the x-axis at the location of each sample (default TRUE).
col_pos	Graphical parameter for the barplot. Colour of all the positive values (default black).
col_neg	Graphical parameter for the barplot. Colour of all the negative values (default light grey).
title	Name to be added on top of the plot (default NA).
src	A graphical parameter used by the plot_loo() function.

Value

No return value, this function is used to plot.

Examples

data(crest_ex)
plot_diagram(crest_ex, bars=TRUE, col='black', bar_width=0.8)
plot_diagram(crest_ex,  col=1:7, tickAtSample=FALSE)
#> Replace 'tempdir()' by the location where the sample should be saved (e.g. 'getwd()')
plot_diagram(crest_ex, save=TRUE,
             filename=file.path(tempdir(), 'testDiagram.pdf'),
             bars=TRUE, col_pos='cornflowerblue', col_neg='darkgreen',
             bar_width=0.8, xlim=c(3,15))

mchevalier2/crestr documentation built on Feb. 14, 2025, 6:31 p.m.