subniche (version 1.5)

plot.subniche: Summarizes the results of the species subniche

Description

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

Usage

# S3 method for 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,
  fac.var.lab = 1.2,
  col.var = "black",
  col.su = "black",
  col.G_k = "red",
  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 = "black",
  col.K = "#2c7fb8",
  lty.K = 1,
  show.lines = F,
  ...
)

Arguments

x

an object of class subniche.

xax

column for abscissas.

yax

column for ordinate.

ax.angle.arrow

arrow angle head for plot labeled "Axes", see arrows for more details.

ax.col.arrow

arrow color for plot labeled "Axes", see arrows for more details.

ax.length.arrow

arrow head length for plot labeled "Axes", see arrows for more details.

ax.lwd.arrow

arrow width for plot labeled "Axes", see arrows for more details.

ax.leg.posi

legend position for plot labeled "Axes", see legend for more details.

ax.leg.cex

legend size label for plot labeled "Axes", see legend for more details.

eig.col.chos

bar color for the selected components for plot labeled "Eigenvalues".

eig.col.left

bar color for the component leftover for plot labeled "Eigenvalues".

eig.leg.posi

legend position for plot labeled "Eigenvalues", see legend for more details.

eig.leg.cex

legend size label for plot labeled "Eigenvalues"", see legend for more details.

su.leg.posi

legend position for plot labeled "SU", see legend for more details.

su.leg.cex

legend size label for plot labeled "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 labeled "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 labeled "Variables and Species", see arrows for more details.

var.angle.arrow

variables arrow angle head for plot labeled "Variables and Species", see arrows for more details.

var.leg.posi

legend position for plot labeled "Variables and Species", see legend for more details.

var.leg.cex

legend size label for plot labeled "Variables and Species", see legend for more details.

fac.var.lab

factor for moving the variable labels from its original coordinates for clarity, by defaults they are multiply 1.2

col.var

color variables labels, 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.

nic.leg.posi

legend position for plot labeled "Niches", see legend for more details.

nic.leg.cex

legend size label for plot labeled "Niches", see legend for more details.

sub.leg.cex

legend size label for plot labeled "Subsets"", see legend for more details.

sub.leg.posi

legend position for plot labeled "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.

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)