make_ggplot: Convert geomorph plots to ggplot objects

In EmSherratt/geomorph: Geometric Morphometric Analyses of 2D/3D Landmark Data

Convert geomorph plots to ggplot objects

Description

Function attempts to coerce plot information from a geomorph plot object to an amenable ggplot object.

Usage

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.

Author(s)

Michael Collyer

Examples

### 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)

EmSherratt/geomorph documentation built on June 24, 2022, 11:05 p.m.