shapeHulls | R Documentation |
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.
shapeHulls(
x,
groups = NULL,
group.cols = NULL,
group.lwd = NULL,
group.lty = NULL
)
x |
A |
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. |
This function is a wrapper for the points
function. It is intentionally limited, so
as to not interfere with other plot parameter adjustments.
Michael Collyer
procD.lm
## 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))
## End(Not run)
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