cati (version 0.99.3)

plotDistri: Plot function to represent density of trait values

Description

Plot function to represent density of trait values

Usage

plotDistri(traits = NULL, var.1 = NULL, var.2 = NULL, col.dens = NULL, 
	plot.ask = TRUE, ylim.cex = 1, cex.leg = 0.8, polyg = TRUE, 
	multipanel = TRUE, leg = TRUE, xlim = NULL, ylim = NULL, 
	main = "default", ...)

Arguments

traits

Matrix of traits with traits in column.

var.1

The first variable defines the division of each plots, in most case either a vector of species or name of sites.

var.2

The second variable define the division by color, in most case either a vector of species or name of sites.

col.dens

A vector of colors for the second variable.

plot.ask

Logical value; ask for plotting the next plot or not.

ylim.cex

Numeric value; the magnification to be used for range of y axe

cex.leg

Numeric value; the magnification to be used for legend relative to the current setting of cex

polyg

Logical value; do the mean distribution is full or empty

multipanel

Logical value. If TRUE divides the device to shown several traits graphics in the same device.

leg

Logical value; if TRUE print the legend.

ylim

Numeric vectors of length 2, giving the y coordinates range

xlim

Numeric vectors of length 2, giving the y coordinates range

main

Title for the plot. Default set automatic title using informations in the input dataset.

…

Any additional arguments are passed to the plot function creating the core of the plot and can be used to adjust the look of resulting graph.

Value

None; used for the side-effect of producing a plot.

See Also

plotSpPop

Examples

# NOT RUN {
data(finch.ind)

# }
# NOT RUN {
	#Plot the distribution of trait values for populations, 
	#species, sites and regional scales. 
	
	### First, let try the distribution for all populations 
	#of Darwin finches.
	
	par(mfrow = c(4,4), cex = 0.5)
	plotDistri(traits.finch, sp.finch, ind.plot.finch, ylim.cex = 3, 
	plot.ask = FALSE, multipanel = FALSE, leg = FALSE)
	
	### Then we can inverse the second and the third arguments 
	#to plot the distribution for all finches species. 
	
	par(mfrow = c(4,4), cex = 0.5)
	plotDistri(traits.finch, ind.plot.finch, sp.finch, ylim.cex = 8, 
	plot.ask = FALSE, multipanel = FALSE, leg = FALSE)
	
	### Only one trait to plot using leg = TRUE to plot the legend

	par(mfrow=c(2,3))
	plotDistri(as.matrix(traits.finch[,1]), ind.plot.finch, sp.finch, 
    ylim.cex=8, plot.ask = FALSE, multipanel = FALSE, leg = TRUE, cex.leg=0.5)

	### You can also plot trait distribution for all species in the region
	
	par(mfrow = c(1,1), cex = 1)
	plotDistri(traits.finch, rep("region", times = dim(traits.finch)[1]), 
	sp.finch, ylim.cex = 6, plot.ask = FALSE, leg = FALSE)
	
	### You can also plot trait distribution for all sites
	#without taking into account species identity

	plotDistri(traits.finch, rep("toutes_sp", times = dim(traits.finch)[1]), 
	ind.plot.finch, ylim.cex = 3, plot.ask = FALSE)

# }
# NOT RUN {
	
# }