geomorph: shapeHulls – R documentation

Become an expert in R — Interactive courses, Cheat Sheets, certificates and more!

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. 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

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))

geomorph

Geometric Morphometric Analyses of 2D/3D Landmark Data

v4.0.0

GPL (>= 2)

Authors

Dean Adams [aut, cre], Michael Collyer [aut], Antigoni Kaliontzopoulou [aut], Erica Baken [aut]

Initial release