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### Script for morphological data treatment and plotting  																											###
### Written by V. Fischer, P. Wintgens, Feb 2025          																											###
### Associated paper: Fischer, Weis et al. Vampyromorph coleoid predation by an ichthyosaurian from the Early Jurassic Lagerstätte of Bascharage, Luxembourg. PeerJ	###
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### Packages
library(ggplot2)
library(readxl)
library(tidyr)
library(viridis)

### Get and tidy data
raw_data <- read_excel("morpho_data.xlsx",na="NA",sheet="Dataset")
#raw_data$Total_length <- log(raw_data$Total_length) #log transforms body length, if needed
data <- pivot_longer(raw_data,!Species, names_to="Trait", values_to="Value")
data$Trait <- factor(data$Trait, levels=colnames(raw_data)[-1])

### Make the barplots

clade_colors<-c("#25BA8C", viridis(n=7, option="E")[c(6, 5)])
barplot(rep(1, length(clade_colors)), col=clade_colors, border=NA, space=0) #visualise the colors
names(clade_colors)<-raw_data$Species #"Stenopterygius_triscissus","Pachycormus_macropterus","Saurostomus_esocinus"

ggplot(data,aes(x=Species, y=Value,fill=Species)) +
  geom_col() +  
  facet_wrap(~Trait, scales="free_x",ncol=1)+
  scale_fill_manual(values=clade_colors)+
  coord_flip()+
  xlab("")+
  ylab("")+
  ggtitle(label="Comparison of functional traits")+
  theme(panel.grid=element_blank(), panel.background=element_rect(fill="white"), axis.text.y=element_blank(),
        axis.ticks.y=element_blank(),strip.background=element_rect(fill="white"), 
        legend.position="bottom")
  #theme_void()

ggsave("morpho_data.pdf",device="pdf",width=90,height=250,units="mm")