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

In subniche: Within Outlying Mean Indexes: Refining the OMI Analysis

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)

subniche documentation built on July 15, 2022, 5:05 p.m.