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Plot function to represent density of trait values

plotDistri.Rd

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.

Author

Adrien Taudiere

See also

plotSpPop

Examples

data(finch.ind)

if (FALSE) { # \dontrun{
  #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)

} # }