### Script designed by Yann Gager for morphometry of Molossus
### http://journals.plos.org/plosone/article?id=10.1371/journal.pone.0150780

### Download packages
require(ggplot2)
require(gridExtra)
require(MASS)


## Download your dataset (here called "combin")
## Replace the variables in the graph ("mass_of_bat","FA","species")
## Replace colors coded manually(scale_colour_manual & scale_fill_manual)


#scatterplot of x and y variables
### Placeholder plot - prints nothing at all
empty <- ggplot() + geom_point(aes(1,1), colour="white") + theme(plot.background = element_blank(), panel.grid.major = element_blank(), panel.grid.minor = element_blank(), panel.border = element_blank(), panel.background = element_blank(), axis.title.x = element_blank(), axis.title.y = element_blank(), axis.text.x = element_blank(), axis.text.y = element_blank(), axis.ticks = element_blank(),axis.line = element_line(colour = "white"))

scatter3sp <- ggplot(combin,aes(mass_of_bat, FA)) + geom_point(aes(colour=species)) + scale_colour_manual(values = c("#00FF99","blue","orange"),name="Species",labels=c("M. bondae","M. coibensis","M. molossus")) + theme(legend.position=c(1,1),legend.direction="horizontal",legend.justification=c(1,1),axis.title.x = element_text(face="bold"),axis.title.y = element_text(face="bold"),axis.line = element_line(colour = "black"),panel.background = element_rect(fill="white"),legend.background = element_rect(fill="white"),legend.key = element_rect(fill="white"),legend.text = element_text(face="italic")) + xlab("Mass (g)") + ylab("Forearm length (mm)") #+ scale_shape_discrete(name="Sex") #Green for currentium: "#009E73" / 
scatter3sp

#marginal density of x - plot on top
plot_top3sp <- ggplot(combin, aes(mass_of_bat, fill=species)) + 
  geom_density(alpha=.5) + 
  scale_fill_manual(values = c("#00FF99", "blue", "orange")) + 
  theme(legend.position = "none",panel.background = element_rect(fill="white"),axis.line = element_line(colour = "black")) + xlab("") + ylab("")

#marginal density of y - plot on the right
plot_right3sp <- ggplot(combin, aes(FA, fill=species)) + 
  geom_density(alpha=.5) + 
  coord_flip() + 
  scale_fill_manual(values = c("#00FF99","blue","orange")) + 
  theme(legend.position = "none",panel.background = element_rect(fill="white"),axis.line = element_line(colour = "black")) + xlab("") + ylab("")

#arrange the plots together, with appropriate height and width for each row and column
pdf("C:/Users/ygager/Desktop/PHD/WRITING/2-Diversity/FIGURES/Morpho-2K+cur.pdf",width=14,height=8)
combiplot3sp  <- grid.arrange(plot_top3sp, empty, scatter3sp, plot_right3sp, ncol=2, nrow=2, widths=c(4, 1), heights=c(1.5, 4))
dev.off()