subniche (version 1.5)

subplot: Sub-community plot under each sub-environmental space K

Description

The function to represent the community subniche position under each subenvironment K with their respective marginality from Gk.

Usage

subplot(
  subnic,
  main = NULL,
  sig = NULL,
  sig_thres = 0.05,
  xlab = NULL,
  ylab = NULL,
  col.axis = "azure3",
  lty.axis = 2,
  lwd.axis = 2,
  pch.SR.pos = 21,
  cex.SR.pos = 1,
  col.SR.pt = "black",
  col.SR.pos = "#ffa600",
  col.SR.lab = "black",
  cex.SR.lab = NA,
  fac.SR.lab = 1.2,
  border.E = "black",
  col.E = "#92c5de",
  lty.E = 1,
  lwd.E = 1,
  border.K = "black",
  col.K = "#2c7fb8",
  lty.K = 1,
  lwd.K = 1,
  col.arrow = "black",
  angle.arrow = 20,
  lwd.arrow = 2,
  length.arrow = 0.1,
  col.Gk.pos = "red",
  col.Gk.pt = "black",
  cex.Gk.pos = 1,
  pch.Gk.pos = 21,
  col.su = "#b35806",
  pt.su = "black",
  cex.su = 0.7,
  pch.su = 1,
  font.sp = 2,
  leg = T,
  posi.leg = "topleft",
  bty.leg = "n",
  ...
)

Arguments

subnic

an object of class subniche.

main

a main title for the plot, see title for more details.

sig

a factor defining the significance species, default NULL.

sig_thres

value for minimum significance, default 0.05

xlab

a label for the x axis, defaults to a description of x, see title for more details.

ylab

a label for the y axis, defaults to a description of y, see title 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.

pch.SR.pos

type of the point representing SR position, see points for more details.

cex.SR.pos

size of the point representing SR position, see points for more details.

col.SR.pt

point color contour if pch=21:25.

col.SR.pos

color of the point representing SR position, see points for more details.

col.SR.lab

color of the species labels, see see text for more details.

cex.SR.lab

size of the species labels defautls NA for no labels, see see text for more details.

fac.SR.lab

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

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.

lwd.E

line width 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.

lwd.K

line width for the K border, see polygon for more details.

col.arrow

arrow color, see arrows for more details.

angle.arrow

arrow angle head, see arrows for more details.

lwd.arrow

arrow width, see arrows for more details.

length.arrow

arrow head length, see arrows for more details.

col.Gk.pos

color of the point representing Gk, see points for more details.

col.Gk.pt

point color contour if pch=21:25.

cex.Gk.pos

size of the point representing Gk, see points for more details.

pch.Gk.pos

type of the point representing Gk, see points for more details.

col.su

color of the points representing the sampling units (SU), see points for more details.

pt.su

point color contour if pch=21:25.

cex.su

size of the points representing the sampling units (SU), see points for more details.

pch.su

type of the points representing the sampling units (SU), see points for more details.

font.sp

font of the species labels, see see text for more details.

leg

a logical option for legend to be plotted or not, default leg=T.

posi.leg

legend location in the graph, see legend for more details.

bty.leg

the type of box to be drawn around the legends. The allowed values are "o" (the default) and "n". See legend for more details

...

further arguments passed to or from other methods.

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$ls)[1]
#Create a factor which defines the subsets
fact <- factor(c(rep(1,N/2),rep(2,N/2)))
# nic1 will be use as reference and fact will be use to define the subniches environment
subnic1 <- subniche(nic1, fact)
#Two graphs are drawn one after the other
siggk <- rtestsubor(subnic1,10)
sig = c(siggk$`1`$witomigktest$subni.pvalue[-28],siggk$`2`$witomigktest$subni.pvalue[-28])
subplot(subnic1, sig = sig, sig_thres= 0.1)