geomorph (version 3.1.2)

shapeHulls: Update Plots with Convex Hulls for Groups

Description

This function is used to update plot.procD.lm and plot.gm.prcomp ordination plot objects with convex hulls for different groups. This function does not currently work with plotTangentSpace. If no groups are defined (groups is NULL) just a single convex hull will be returned. Groups do not need to be a factor in the original procD.lm fit.

Usage

shapeHulls(x, groups = NULL, group.cols = NULL, group.lwd = NULL,
  group.lty = NULL)

Arguments

x

A plot.procD.lm or plot.gm.prcomp plot object.

groups

An optional vector or factor to define groups for hull. If NULL, only one hull will be generated for all points.

group.cols

An optional vector to define hull colors, arranged in the same order as factor levels. If NULL and if multiple groups exist, the general R color sequence (black, red, green, blue, etc.) will be used.

group.lwd

An optional vector equal in length to the number of group levels, and arranged in the order of group levels, to modify hull line width.

group.lty

An optional vector equal in length to the number of group levels, and arranged in the order of group levels, to modify hull line type.

Details

This function is a wrapper for the points function. It is intentionally limited, so as to not interfere with other plot parameter adjustments.

See Also

procD.lm

Examples

# NOT RUN {
# Via procD.lm and plot.procD.lm

data("pupfish")
gdf <- geomorph.data.frame(coords = pupfish$coords, Sex = pupfish$Sex,
Pop = pupfish$Pop)
fit <- procD.lm(coords ~ Pop * Sex, data = gdf, print.progress = FALSE)
pc.plot <- plot(fit, type = "PC", pch = 19)
shapeHulls(pc.plot)

pc.plot <- plot(fit, type = "PC", pch = 19)
groups <- interaction(gdf$Pop, gdf$Sex)

shapeHulls(pc.plot, groups = groups, 
group.cols = c("dark red", "dark red", "dark blue", "dark blue"),
group.lwd = rep(2, 4), group.lty = c(2, 1, 2, 1))

legend("topright", levels(groups), 
col = c("dark red", "dark red", "dark blue", "dark blue"),
lwd = rep(2,4), lty = c(2, 1, 2, 1))

pc.plot <- plot(fit, type = "PC", pch = 19)
shapeHulls(pc.plot, groups = gdf$Sex, group.cols = c("black", "black"), 
group.lwd = rep(2, 2), group.lty = c(2, 1))
legend("topright", levels(gdf$Sex), lwd = 2, lty = c(2, 1))

# Via gm.prcomp and plot.gm.prcomp

data(plethspecies) 
Y.gpa <- gpagen(plethspecies$land)    #GPA-alignment
pleth.phylo <- gm.prcomp(Y.gpa$coords, phy = plethspecies$phy)
summary(pleth.phylo)

pc.plot <- plot(pleth.phylo, phylo = TRUE)
gp <- factor(c(rep(1, 5), rep(2, 4)))
shapeHulls(pc.plot, groups = gp, group.cols = 1:2, 
group.lwd = rep(2, 2), group.lty = c(2, 1))
legend("topright", c("P. cinereus clade", "P. hubrichti clade"), 
col = 1:2, lwd = 2, lty = c(2, 1))
# }