Momocs (version 0.2-6)

morpho.space: Calculate and plots morphological spaces.

Description

Calculates and plots morphological spaces with many options.

Usage

morpho.space(dudi, xax = 1, yax = 2, xlim, ylim, nb.pts = 300,
                 pos.shp = c("li", "circle", "range")[3], nr.shp = 6,
                 nc.shp = 5, amp.shp = 1, scale.shp = 1, rotate.shp =
                 0, circle.nb.shp = 12, circle.r.shp, plot = TRUE,
                 layer = TRUE, col.shp = "#70809011", border.shp =
                 "#708090", pch.pts = 20, col.pts = "grey40",
                 first.point = FALSE)

Arguments

dudi

a dudi.pca object.

xax

integer. The index of the first PC axis to use.

yax

integer. The index of the first PC axis to use.

xlim

A vector of 2 numeric indicating the x-range.

ylim

A vector of 2 numeric indicating the y-range.

nb.pts

The number of points to calculate.

pos.shp

character, any of the ("li", "circle", "range") methods. It specifies the way shapes have to be drawn. "li" draws shapes on the actual positions on the factorial map ; "circle" draws shapes on a circle w

nr.shp

numeric. The number of shape rows.

nc.shp

numeric. The number of shape columns.

amp.shp

numeric. An amplifying factor for shape deformation.

scale.shp

numeric. The size of shapes, relatively to 1/8 of the highest range (x or y).

rotate.shp

numeric. If specified, the angles (in radians) to counter-clockwise rotate shapes plotted.

circle.nb.shp

integer. When pos == "circle", the number of shapes on the circle.

circle.r.shp

numeric. When pos == "circle", the circle radius.

plot

logical. Whether to plot or not the morphological space.

layer

logical. Whether to add calculated shapes on an existing plot. Used for instance by dudi.plot.

col.shp

A color string for filling the shapes.

border.shp

A color string for shape borders.

pch.pts

A pch for plotting the points from the dudi-class object. Use NA to not display these points.

col.pts

A color to plot these points.

first.point

logical. Whether to draw or not the first point of the shapes.

Details

Note that tFourier analyses since the reconstruction of shapes do not always lead to closed shapes (see Rohlf F, Archie J. 1984. A comparison of Fourier methods for the description of wing shape in mosquitoes (Diptera: Culicidae). Systematic Biology: 302-317.)

See Also

dudi.plot.

Examples

data(bot)
botF <- eFourier(bot)
botD <- pca(botF)
morpho.space(botD)