plot.subniche | R Documentation |
The function plot the resulting species subniche of the WitOMI calculation.
## 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, 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, ... )
x |
an object of class |
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. |
The function illustrate the results of subniche calculation with a great deal of customization parameters.
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)
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