library(ggplot2)
library(scales)
library(gridExtra)
library(grid)


##################
### BAR COLORS ###
##################

gg_color_hue <- function(n) {
  hues = seq(15, 375, length = n + 1)
  hcl(h = hues, l = 65, c = 100)[1:n]
}
cols = gg_color_hue(7)

hapog      = cols[1]
hypo       = cols[2]
nextpolish = cols[3]
ntedit     = cols[4]
pilon      = cols[5]
polca      = cols[6]
racon      = cols[7]

#######################
### DATA FORMATTING ###
#######################

dat = read.csv('PolishingAfterOneRoundOfHapoG')
colnames(dat)[1] = "Tool"
dat$Tool = factor(dat$Tool, levels=c("Uncorrected", "Hapo-G+Hapo-G", "HyPo+Hapo-G", "NextPolish+Hapo-G", "ntEdit+Hapo-G", "Pilon+Hapo-G", "POLCA+Hapo-G", "Racon+Hapo-G"))

#####################
### MAPPED PAIRS  ###
#####################

ppair_top = ggplot(data=dat, aes(x=Tool, y=perfectPairs)) +
  geom_col(position=position_dodge2(width = 0.9, preserve = "single"), color="black", fill=c(hypo, nextpolish, ntedit, pilon, polca, racon)) +
  theme_bw() +
  theme(axis.text = element_text(size = 16), axis.title = element_text(size = 16),legend.text = element_text(size = 20),plot.title = element_text(size = 20)) +
  theme(legend.position = "none")+
  xlab("") +
  ylab("") +
  scale_y_continuous(breaks=c(0, 45000000, 46000000, 47000000, 48000000,49000000,50000000), labels=c("0", "45", "46", "47", "48", "49", "50")) +
  coord_cartesian(ylim=c(45000000, 49500000))

ppair_bottom = ggplot(data=dat, aes(x=Tool, y=perfectPairs)) +
  geom_col(position=position_dodge2(width = 0.9, preserve = "single"), color="black", fill=c(hypo, nextpolish, ntedit, pilon, polca, racon)) +
  theme_bw() +
  theme(axis.text = element_text(size = 16), axis.title = element_text(size = 16),legend.text = element_text(size = 20),plot.title = element_text(size = 20)) +
  theme(legend.position = "none")+
  xlab("") +
  ylab("") +
  scale_y_continuous(breaks=c(0, 10000000, 20000000, 30000000, 40000000, 50000000), labels=c("0", "10", "20", "30", "40", "50"))

fig <- grid.arrange(ppair_top, ppair_bottom,
                      heights=c(2, 3),
                      ncol=1, nrow=2,
                      left=textGrob("Million of perfectly mapped pairs",
                                    rot=90,
                                    vjust=1,
                                    gp = gpar(fontsize = 24)))

ggsave(file="Figure_S2.png", plot=fig, width=16, height=9)