plot.subniche: Summarizes the results of the species subniche

In KarasiewiczStephane/WitOMI: Within Outlying Mean Indexes: Refining the OMI Analysis

Description

The function plot the resulting species subniche of the WitOMI calculation.

Usage

## S3 method for class 'subniche'
plot(
  x,
  xax = 1,
  yax = 2,
  ax.angle.arrow = 20,
  ax.col.arrow = "black",
  ax.length.arrow = 0.1,
  ax.lwd.arrow = 1,
  ax.leg.posi = "bottomleft",
  ax.leg.cex = 1.2,
  eig.col.chos = "black",
  eig.col.left = "gray",
  eig.leg.posi = "topright",
  eig.leg.cex = 1.2,
  su.leg.posi = "bottomleft",
  su.leg.cex = 1.2,
  col.axis = "azure3",
  lty.axis = 2,
  lwd.axis = 2,
  var.col.arrow = "black",
  var.length.arrow = 0.1,
  var.lwd.arrow = 1,
  var.angle.arrow = 20,
  var.leg.posi = "bottomleft",
  var.leg.cex = 1.2,
  col.var = "black",
  col.sp = rainbow(n = dim(x$li)[1]),
  col.su = "black",
  col.G_k = "red",
  col.ax = "black",
  nic.leg.posi = "bottomleft",
  nic.leg.cex = 1.2,
  sub.leg.cex = 1.2,
  sub.leg.posi = "bottomleft",
  pch.su = 16,
  cex.su = 1,
  border.E = "#92c5de",
  col.E = "#92c5de",
  lty.E = 1,
  border.K = "#fdb462",
  col.K = "#fdb462",
  lty.K = 1,
  lty.NR = 1,
  sub.angle.arrow = 20,
  sub.col.arrow = "black",
  sub.length.arrow = 0.1,
  sub.lwd.arrow = 1,
  show.lines = F,
  ...
)

Arguments

x	an object of class subniche.
xax	column for abscisse.
yax	column for ordinate.
ax.angle.arrow	arrow angle head for plot labelled "Axes", see arrows for more details.
ax.col.arrow	arrow color for plot labelled "Axes", see arrows for more details.
ax.length.arrow	arrow head length for plot labelled "Axes", see arrows for more details.
ax.lwd.arrow	arrow width for plot labelled "Axes", see arrows for more details.
ax.leg.posi	legend position for plot labelled "Axes", see legend for more details.
ax.leg.cex	legend size label for plot labelled "Axes", see legend for more details.
eig.col.chos	bar color for the selected components for plot labelled "Eigenvalues".
eig.col.left	bar color for the component leftover for plot labelled "Eigenvalues".
eig.leg.posi	legend position for plot labelled "Eigenvalues", see legend for more details.
eig.leg.cex	legend size label for plot labelled "Eigenvalues"", see legend for more details.
su.leg.posi	legend position for plot labelled "SU", see legend for more details.
su.leg.cex	legend size label for plot labelled "SU", see legend for more details.
col.axis	axis color, see par for more details.
lty.axis	axis line type, see par for more details.
lwd.axis	axis width, see par for more details.
var.col.arrow	variables arrow color for plot labelled "Variables and Species", see arrows for more details.
var.length.arrow	variables arrow length of the edges of the arrow head (in inches).
var.lwd.arrow	variables arrow width for plot labelled "Variables and Species", see arrows for more details.
var.angle.arrow	variables arrow angle head for plot labelled "Variables and Species", see arrows for more details.
var.leg.posi	legend position for plot labelled "Variables and Species", see legend for more details.
var.leg.cex	legend size label for plot labelled "Variables and Species", see legend for more details.
col.var	color variables labels, see textplot for more details.
col.sp	color species labels and their respective niches, see textplot for more details.
col.su	color of sampling units, see points for more details.
col.G_k	color label G_k, see textplot for more details.
col.ax	color of axes labels, see textplot for more details.
nic.leg.posi	legend position for plot labelled "Niches", see legend for more details.
nic.leg.cex	legend size label for plot labelled "Niches", see legend for more details.
sub.leg.cex	legend size label for plot labelled "Subsets"", see legend for more details.
sub.leg.posi	legend position for plot labelled "Subsets", see legend for more details.
pch.su	type of the points representing the sampling units (SU), see points for more details.
cex.su	size of the points representing the sampling units (SU), see points for more details.
border.E	color border of E polygon, see polygon for more details.
col.E	inside color of E polygon, see polygon for more details.
lty.E	line type for the E border, see polygon for more details.
border.K	color border of K polygon, see polygon for more details.
col.K	inside color of K polygon, see polygon for more details.
lty.K	line type for the K border, see polygon for more details.
lty.NR	line type for the NR border, see polygon for more details.
sub.angle.arrow	arrow angle head for plot labelled "Subsets", see arrows for more details.
sub.col.arrow	arrow color for plot labelled "Subsets", see arrows for more details.
sub.length.arrow	arrow head length for plot labelled "Subsets", see arrows for more details.
sub.lwd.arrow	arrow width for plot labelled "Subsets", see arrows for more details.
show.lines	if true, then lines are plotted between x,y and the word, for those words not covering their x,y coordinates. See textplot for more details.
...	further arguments passed to or from other methods.

Details

The function illustrate the results of subniche calculation with a great deal of customization parameters.

Examples

library(subniche)
data(doubs)
dudi1 <- dudi.pca(doubs$env, scale = TRUE, scan = FALSE, nf = 3)
nic1 <- niche(dudi1, doubs$fish, scann = FALSE)
# number of sites
N <- dim(nic1$ls)[1]
#Create a factor which defines the subsets
fact <- factor(c(rep(1,N/2),rep(2,N/2)))
# nic1 will be use as reference and fact will be use to define the subniches environment
subnic1 <- subniche(nic1, fact)
plot(subnic1)

KarasiewiczStephane/WitOMI documentation built on March 31, 2020, 3:40 p.m.