# Convert geomorph plots to ggplot objects Function attempts to coerce plot information from a geomorph plot object to an amenable ggplot object. ```r make_ggplot(object) ``` ## Arguments - `object`: A plot object produced from `plot.gm.prcomp`, `plot.pls`,`plot.procD.lm`, or `plotAllometry`. For `plot.procD.lm` objects, only types "PC" or "regression" should work. ## Details This function will attempt to use the plot arguments from an geomorph plot object to make a ggplot that can be additionally updated, as desired. Not all plot characteristics might be converted. Nonetheless, a ggplot will be coerced and could be updated, according to user preference. This function assumes no responsibility for arguments made by `ggplot`. It merely produces a ggplot object that should resemble a geomorph plot default. Any augmentation of ggplot objects can be done either by direct intervention of the ggplot produced or reformatting the initial geomorph plot produced. One should not expect direct correspondence between R base plot parameters and ggplot parameters. ## Examples ```r ## Not run: ### PLS Example data(plethodon) Y.gpa <- gpagen(plethodon$land) #GPA-alignment landmarks on the skull and mandible assigned to partitions land.gps <- c("A","A","A","A","A","B","B","B","B","B","B","B") IT <- integration.test(Y.gpa$coords, partition.gp = land.gps, iter = 999) summary(IT) # Test summary P <- plot(IT) # PLS plot make_ggplot(P) # same plot in ggplot ### Allometry example data(plethodon) Y.gpa <- gpagen(plethodon$land, print.progress = FALSE) #GPA-alignment gdf <- geomorph.data.frame(Y.gpa, site = plethodon$site, species = plethodon$species) fit <- procD.lm(coords ~ Csize * species * site, data=gdf, iter=0, print.progress = FALSE) P <- plotAllometry(fit, size = gdf$Csize, logsz = TRUE, method = "PredLine", pch = 19, col = as.numeric(interaction(gdf$species, gdf$site))) make_ggplot(P) ### Tangent Space plot data(plethspecies) Y.gpa <- gpagen(plethspecies$land) #GPA-alignment PCA.w.phylo <- gm.prcomp(Y.gpa$coords, phy = plethspecies$phy) P <- plot(PCA.w.phylo, phylo = TRUE, main = "PCA.w.phylo") make_ggplot(P) ## End(Not run) ``` ## Author(s) Michael Collyer

make_ggplot function