shapeHulls: Update Plots with Convex Hulls for Groups

In EmSherratt/geomorph: Geometric Morphometric Analyses of 2D/3D Landmark Data

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. 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.

Author(s)

Michael Collyer

See Also

procD.lm

Examples

# 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))

EmSherratt/geomorph documentation built on June 24, 2022, 11:05 p.m.