subplot: Sub-community plot under each sub-environmental space K
In polak51/WitOMI: Within Outlying Mean Indexes: Refining the OMI Analysis

Description Usage Arguments Examples

View source: R/subplot.R

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

subplot(subnic, main=NULL, xlab=NULL, ylab=NULL, col.axis="azure3", lty.axis=2,
       lwd.axis=2, col.sublab="black", font.sublab=2, cex.sublab=0.7, show.lines=F,
       border.E="#92c5de", col.E="#92c5de", lty.E=1, lwd.E=1, border.K ="#2c7fb8",
       col.K ="#2c7fb8", lty.K=1, lwd.K=1, col.arrow="black", angle.arrow=20, lwd.arrow=2,
       length.arrow=0.1, col.G_k= "#b35806", cex.G_k=0.5, pch.G_k=19,
       col.su="#b35806", cex.su=0.5, pch.su=1, posi.leg="topleft", bty.leg="n", ...)

`subnic`	an object of class `subniche`.
`main`	a main title for the plot, see title for more details.
`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.
`col.sublab`	color of the species labels, see textplot for more details.
`font.sublab`	font of the species labels, see textplot for more details.
`cex.sublab`	size of the species labels, see textplot 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.
`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.G_k`	color of the point representing G_k, see points for more details.
`cex.G_k`	size of the point representing G_k, see points for more details.
`pch.G_k`	type of the point representing G_k, see points for more details.
`col.su`	color 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.
`pch.su`	type of the points representing the sampling units (SU), see points for more details.
`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.

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$ls)[1]
#Create a factor which defines the subsets
fact <- factor(c(rep(1,N/2),rep(2,N/2)))
# nic1 will be use as reference and fact will be use to define the subniches environment
subnic1 <- subniche(nic1, fact)
eig <- round(subnic1$eig/sum(subnic1$eig)*100,2)[1:2]
#Two graphs are drawn one after the other
subplot(subnic1,main="Species subniche in K",
xlab=paste(paste("OMI1", eig[1], sep=" "),"%", sep=""),
ylab=paste(paste("OMI2", eig[2], sep=" "),"%", sep=""))