plot_mo_ind: Plotting function for 'morpho_indices' outputs

In sginot/MorphoInd: Simpsons LSI and Uerpmanns VSI

Plotting function for 'morpho_indices' outputs

Description

Plotting function for 'morpho_indices' outputs

Usage

plot_mo_ind(
  dat = dat,
  name = name,
  ref = 1,
  samp = name[-ref],
  var.names = colnames(dat$LSI.df),
  which.var = 1:length(var.names),
  index = "LSI",
  plot.ref = T,
  plot.index = T,
  bootmean = F,
  bootmedian = F,
  plot.mISD = T,
  CI = F,
  col.ref = "black",
  col = rainbow(length(samp)),
  alpha.lev = 0.2,
  lty.index = 1,
  lty.bootmean = 2,
  lty.bootmed = 3,
  lgnd = T,
  lgnd.pos = "topleft",
  cex.lgnd = 0.5,
  xlab = "Descriptors",
  ylab = index,
  tick.labels = colnames(dfs)
)

Arguments

dat	Data is the output from function morpho.indices().
name	Character vector of names for ALL samples INCLUDING reference.
ref	Index number (or name as character string) of reference sample. Default = 1, so the first sample is assumed to be the reference.
samp	Numeric (or character) vector containing the index numbers (or names) of samples to be plotted. Defaults to all except reference sample.
var.names	Character vector containing the names of ALL morphological descriptors. By default the column names of data frame from the "dat" argument.
which.var	Numeric (or character) vector specifying the morphological descriptors to be plotted. By default all of them.
index	Which morphological index will be plotted: "LSI" (default), "VSI" or "VSI2".
plot.ref	Plot reference sample? Default = TRUE
plot.index	Plot original values of LSI, VSI or VSI2. Default = TRUE.
bootmean	Plot average bootstraped value of LSI, VSI or VSI2. Default = FALSE.
bootmedian	Plot median bootstraped value of LSI, VSI or VSI2. Default = FALSE.
plot.mISD	Should mISD values be plotted?
CI	Plot 95 confidence intervals? Default = FALSE.
col.ref	Color for reference sample. Default is "black".
col	Vector of colors for samples to be plotted. Length must be equal to length(samp).
alpha.lev	Opacity level (0 = transparent, 1 = opaque). Requires packages 'scales'.
lty.index,	lty.bootmean, lty.bootmed Line types for index, bootstrap mean and bootstrap median, respectively.
lgnd	Plot legend? Default=TRUE.
lgnd.pos	Position of legend, can be specified as for function legend(). Default = 'topleft'.
cex.lgnd	Size of legend. Default = 0.5.
xlab,	ylab As for standard 'plot'.
tick.labels	Labels for tickmarks.

sginot/MorphoInd documentation built on Jan. 27, 2024, 1:32 a.m.