Convert geomorph plots to ggplot objects
Function attempts to coerce plot information from a geomorph plot object to an amenable ggplot object.
make_ggplot(object)
object |
A plot object produced from |
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.
Michael Collyer
### 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)Please choose more modern alternatives, such as Google Chrome or Mozilla Firefox.