Momocs (version 0.1-01)

morph.sp: Plots the morphological space.

Description

Given a matrix of harmonic coefficients, a Nef-object, calculates and plots morphological space i.e. reconstructed shapes using and distributed on the orthonormal set defined by Principal Component axes.

Usage

morph.sp(Nef,
           PCa = 1, PCb = 2, nb.PCa = 5, nb.PCb = 6, fac = NA, 
           morph.sp.extend = 1, zoom.extend = 1.2, asp,
           pch = 20, shp.col = NA, shp.lwd = 1, shp.size, col = "grey40", 
		   ell = FALSE, r = 1, lwd = 1, title = "Morphological space")

Arguments

Nef

the Nef object

PCa

a numeric indicating the first Principal Component axis on which to reconstruct shape

PCb

a numeric indicating the second Pricipal Component axis on which to reconstruct shape

nb.PCa

a numeric indicating how many shape to reconstruct on the first PC axis considered

nb.PCb

a numeric indicating how many shape to reconstruct on the second PC axis considered

fac

a factor indicating the grouping desing

morph.sp.extend

integer how much to extend morphological space reconstruction beyond range on the first PC considered

zoom.extend

integer indicating how much to extend the graphical window

asp

numeric and optionnal indicating the asp of the plotting window

pch

integer or a character indicating the pch for each groups to plot

shp.col

integer or a character indicating the col of these shapes

shp.lwd

numeric indicating the lwd of these shapes borders

shp.size

numeric for fine-tuning of shapes size

col

integer or a character indicating the col for each confidence ellipse to plot

ell

logical indicating whether to draw confidence ellipses for every group

r

numeric indicating the number of standard deviation for confidence ellipses computation

lwd

numeric indicating the lwd for the confidence ellipses

title

character to change the title of the plot

Examples

data(bottles.nef)
fac <- factor(rep(c("beer", "whisky"), each=20))

morph.sp(bottles.nef)
morph.sp(bottles.nef, fac=fac, ell=TRUE)
morph.sp(bottles.nef, fac=fac, nb.PCa=10, nb.PCb=10, ell=TRUE)
morph.sp(bottles.nef, PCa=2, PCb=3)