library(ggplot2)
library(plyr)

args = commandArgs(trailingOnly=TRUE)

lm_eqn = function(plot)
{
    m = lm(count ~ conc, plot);
    eq <- substitute(italic(y) == a + b %.% italic(x)*","~~italic(R)^2~"="~r2,
    list(a = format(coef(m)[1], digits = 2), b = format(coef(m)[2], digits = 2),r2 = format(summary(m)$r.squared, digits = 3)))
    as.character(as.expression(eq));
}

cbPalette <- c("#22635b", "#87bd5b")
plot <- read.table(args[1], header=F, as.is=T, sep="\t")
colnames(plot)<-c("lab","plat", "spikeIn","count", "conc", "type", "category")
plot$count[plot$count == 0] <-0.0001
plot$count=log10(plot$count)
plot$conc=log10(plot$conc)

forE=plot[plot$count > -2.5,]
finalE=forE[forE$conc > -2.5,]

pdf(gsub(".tsv",".pdf",args[1]), bg = "white", width = 7, height = 7)
ggplot(plot, aes(x=conc, y=count, colour=type)) + geom_point(size=5, shape=19, alpha=0.6)+ scale_color_manual(values=cbPalette) + theme_bw() + xlim(-4,5) + ylim(-4,5) + 
xlab("log10(Spike-In concentration)") + ylab ("log10(#reads + 0.0001)") + 
theme(axis.text.x = element_text(size = 16, colour = "black"), axis.text.y = element_text(size = 16,  colour = "black"), legend.text = element_text(size=18), 
      plot.title = element_text(size = 22), legend.title =element_text(size=0, color="white"), axis.title.x = element_text(size = 18), axis.title.y = element_text(size = 18), 
      legend.text.align=0.5, strip.text.x=element_text(size=22), strip.text.y=element_text(size=22)) + theme(legend.position="top") + ggtitle('') + 
      facet_wrap(~ category, ncol=1, scales="free") + geom_smooth(data=finalE,method=lm,se=FALSE,fullrange=TRUE, size=1.5)
dev.off()