subplot_K: Plot sub-environmental space K in E

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

Plot sub-environmental space K in E

Description

The function to represent the sub-environment K in E.

Usage

subplot_K(
  subnic,
  main = NULL,
  xlab = NULL,
  ylab = NULL,
  col.axis = "azure3",
  lty.axis = 2,
  lwd.axis = 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.Gk.pos = "red",
  col.Gk.pt = "black",
  cex.Gk.pos = 1,
  pch.Gk.pos = 21,
  col.Gk.lab = "black",
  cex.Gk.lab = 0.8,
  fac.Gk.lab = 1.5,
  col.su = "#b35806",
  pt.su = "black",
  cex.su = 0.7,
  pch.su = 1,
  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.
xlab	label for x-axis, see title for more details.
ylab	label for y-axis, 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.
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.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.Gk.lab	color of the Gk labels, see see text for more details.
cex.Gk.lab	size of the Gk labels defaults NA for no labels, see see text for more details.
fac.Gk.lab	factor for moving the Gk labels from its original coordinates for clarity, by defaults they are multiply 1.2
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.
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)
#Plot K in E
subplot_K(subnic1)

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