library(readr)
library(ggplot2)
library(gridExtra)
library(ggrepel)


measurements <- read_csv("path/to/file/Suppl_File_2_measurements.csv", 
                              col_types = cols(head_pereon_length = col_number(), 
                                               head_pereon_width = col_number(), 
                                               pleon_telson_length = col_number(), 
                                               pleon_telson_width = col_number()))
df<-as.data.frame(measurements)

df$rel_w <- (pmax(df$head_pereon_width,df$pleon_telson_width))/(df$head_pereon_length+df$pleon_telson_length)
df$ant_post_l <- df$head_pereon_length/df$pleon_telson_length
df$ant_post_w <- df$head_pereon_width/df$pleon_telson_width


#ggplot(df, aes(y=rel_w, x = seq(1, length(df$rel_w)), color=taxon2, group=taxon2))+
  #geom_point()

df$colcon<-with(df, ifelse(age!="triassic",0,1))
df$colcon<-with(df, ifelse(age=="triassic",1,0))


###not really the best combination of axes###
#ggplot(df, aes(y=ant_post_w, x =rel_w , color=taxon2, group=taxon2))+
#  geom_point(data = subset(df, colcon==0), size=2)+
#  scale_x_log10()+
#  scale_y_log10()+
#  geom_text(aes(label=ifelse((age=="triassic"), species, '')), color="black", hjust=-0.05, vjust=-0.05)+
#  scale_color_brewer(palette = "Paired")+
#  geom_point(data = subset(df, colcon==1), color="black", size=2)+
#  theme_bw()

apw_apl <- ggplot(df, aes(y=ant_post_w, x =ant_post_l , color=taxon2, group=taxon2))+
  geom_point(data = subset(df, colcon==0), size=2)+
  scale_x_log10()+
  scale_y_log10()+
  geom_text_repel(
    aes(label=ifelse((age=="triassic"), species, '')),
    color="black",
    nudge_y = 0.2,
    box.padding = 1,
    point.padding = 0,
    segment.color = "grey",
    min.segment.length=0
    )+
  scale_color_brewer(palette = "Paired")+
  geom_point(data = subset(df, colcon==1), color="black", size=2, shape=17)+
  #geom_text(aes(label=ifelse((ant_post_l>10), species,'')))+ #determine the outliers
  #theme_bw()+
  theme(legend.position="none")+
  xlab("Length of the anterior body part relative to the length of the posterior body part")+
  ylab("Width of anterior body part relative to the width of the posterior body part")
  
    
apl_rw <- ggplot(df, aes(y=ant_post_l, x =rel_w , color=taxon2, group=taxon2))+
  labs(color = "Systematic groups")+
  geom_point(data = subset(df, colcon==0), size=2)+
  scale_x_log10()+
  scale_y_log10()+
  geom_text_repel(
    aes(label=ifelse((age=="triassic"), species, '')),
    color="black",
    #nudge_x = -0.2,
    nudge_y = 0.2,
    box.padding = 1,
    point.padding = 0,
    segment.color = "grey",
    min.segment.length=0
    )+
  scale_color_brewer(palette = "Paired")+
  geom_point(data = subset(df, colcon==1), color="black", size=2, shape=17)+
  #geom_text(aes(label=ifelse((rel_w>10), species,'')))+ #determine the outliers
  #theme_bw()+
  xlab("Relative width of the body")+
  ylab("Length of the anterior body part relative to the length of the posterior body part")+
  theme(legend.title=element_text(size=11),
        legend.text=element_text(size=11)
        )

grid.arrange(apw_apl,apl_rw, ncol=2)