ortho.R

#Plot BUSCO with GGPLOT2 


# Load  libraries  
library(ggplot2)  
library("grid")  
 
# Output  
my_output <- paste("busco_figure.svg")   
my_width <- 20  
my_height <- 15  
my_unit <- "cm"  
  
# Colors  
my_colors <- c("#56B4E9", "#3492C7", "#F0E442", "#F04442")  
# Bar height ratio  
my_bar_height <- 0.75  
  
# Legend  
my_title <- "Actinopterigi core orthologs"  
  
# Font  
my_family <- "sans"  
my_size_ratio <- 1  
  
# !!! SEE YOUR DATA HERE !!!   
# Your data as generated by python, remove or add more  
my_species <- c('Cvariegatus', 'Cvariegatus', 'Cvariegatus', 'Cvariegatus', 'Cnevadensis', 'Cnevadensis', 'Cnevadensis', 'Cnevadensis', 'Ctularosa', 'Ctularosa', 'Ctularosa', 'Ctularosa', 'Alinmaeus', 'Alinmaeus', 'Alinmaeus', 'Alinmaeus', 'Preticulata', 'Preticulata', 'Preticulata', 'Preticulata', 'Maculatus', 'Maculatus', 'Maculatus', 'Maculatus')  
my_species <- factor(my_species)  
my_species <- factor(my_species,levels(my_species)[c(length(levels(my_species)):1)]) # reorder your species here just by changing the values in the vector :  
my_percentage <- c(93.6, 1.4, 1.1, 3.9, 70.2, 0.6, 8.8, 20.4, 94.8, 0.7, 1.0, 3.5, 91.6, 1.0, 2.0, 5.4, 94.8, 0.9, 0.9, 3.4, 96.7, 0.8, 0.4, 2.1)  
my_values <- c(3406, 52, 39, 143, 2554, 21, 322, 743, 3452, 26, 35, 127, 3335, 36, 74, 195, 3449, 31, 32, 128, 3519, 28, 13, 80)  
  
######################################  
######################################  
######################################  
# Code to produce the graph  
labsize = 1  
if (length(levels(my_species)) > 10){  
 labsize = 0.66  
}  
print("Plotting the figure ...")  
category <- c(rep(c("S","D","F","M"),c(1)))  
category <-factor(category)  
category = factor(category,levels(category)[c(4,1,2,3)])  
df = data.frame(my_species,my_percentage,my_values,category)  
  
figure <- ggplot() +   
    
  geom_bar(aes(y = my_percentage, x = my_species, fill = category), position = position_stack(reverse = TRUE), data = df, stat="identity", width=my_bar_height) +   
  coord_flip() +   
  theme_gray(base_size = 8) +   
  scale_y_continuous(labels = c("0","20","40","60","80","100"), breaks = c(0,20,40,60,80,100)) +   
  scale_fill_manual(values = my_colors,labels =c(" Complete (C) and single-copy (S)  ",  
                                                 " Complete (C) and duplicated (D)",  
                                                 " Fragmented (F)  ",  
                                                 " Missing (M)")) +     
  ggtitle(my_title) +   
  xlab("") +   
  ylab("\n%BUSCOs") +   
  
  theme(plot.title = element_text(family=my_family, hjust=0.5, colour = "black", size = rel(2.2)*my_size_ratio, face = "bold")) +   
  theme(legend.position="top",legend.title = element_blank()) +   
  theme(legend.text = element_text(family=my_family, size = rel(1.2)*my_size_ratio)) +   
  theme(panel.background = element_rect(color="#FFFFFF", fill="white")) +   
  theme(panel.grid.minor = element_blank()) +   
  theme(panel.grid.major = element_blank()) +  
  theme(axis.text.y = element_text(family=my_family, colour = "black", size = rel(1.66)*my_size_ratio)) +   
  theme(axis.text.x = element_text(family=my_family, colour = "black", size = rel(1.66)*my_size_ratio)) +   
  theme(axis.line = element_line(size=1*my_size_ratio, colour = "black")) +   
  theme(axis.ticks.length = unit(.85, "cm")) +   
  theme(axis.ticks.y = element_line(colour="white", size = 0)) +   
  theme(axis.ticks.x = element_line(colour="#222222")) +   
  theme(axis.ticks.length = unit(0.4, "cm")) +   
  theme(axis.title.x = element_text(family=my_family, size=rel(1.2)*my_size_ratio)) +   
    
  guides(fill = guide_legend(override.aes = list(colour = NULL))) +  
  guides(fill=guide_legend(nrow=2,byrow=TRUE))  
    
  for(i in rev(c(1:length(levels(my_species))))){  
    detailed_values <- my_values[my_species==my_species[my_species==levels(my_species)[i]]]  
    total_buscos <- sum(detailed_values)  
    figure <- figure +   
    annotate("text", label=paste("C:", detailed_values[1] + detailed_values[2], " [S:", detailed_values[1], ", D:", detailed_values[2], "], F:", detailed_values[3], ", M:", detailed_values[4], ", n:", total_buscos, sep=""),   
             y=3, x = i, size = labsize*4*my_size_ratio, colour = "black", hjust=0, family=my_family)  
  }  
    
ggsave(figure, file=my_output, device="svg", width = my_width, height = my_height, unit = my_unit)  
print("Done")