# Update Plots with Convex Hulls for Groups 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. ```r 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. ## Examples ```r ## 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) ``` ## See Also `procD.lm` ## Author(s) Michael Collyer

shapeHulls function