library(ggplot2)
library(plyr)
library(magrittr)
library(dplyr)

args = commandArgs(trailingOnly=TRUE)

lm_eqn = function(plot)
{
    m = lm(count ~ conc, plot);    
    eq = paste0("r2: ", format(summary(m)$r.squared, digits = 3))
    eq
}

cbPalette <- c("#22635b", "#87bd5b")
plot <- read.table(args[1], header=F, as.is=T, sep="\t")
colnames(plot)<-c("sample", "plat", "spikeIn","count", "conc", "type", "lab", "category")
missing = plot[ plot$count == 0, ] %>% group_by(lab, sample) %>% summarize( zeroes = n())
dim(plot)

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,]
dim(finalE)

# text to annotate graphs
graphLabels = data.frame( matrix(nrow = length(unique(plot$lab)), ncol = 3) )
colnames(graphLabels) = c("lab", "sample", "label")

index = 1
for (i in unique(plot$lab))
{
    for (s in unique(plot$sample))
    {
        graphLabels[index, "lab"] = i
        graphLabels[index, "sample"] = s

        definitive = finalE[finalE$lab == i & finalE$sample == s, ]
            
        if ( nrow(definitive) != 0 )
        {
#            graphLabels[index, "label"] = paste0(as.character(as.expression(lm_eqn(definitive))), ", zeroes: ", missing[missing$lab == i & missing$sample == s, "zeroes"])   #r2 computed without zeroes
            graphLabels[index, "label"] = paste0(as.character(as.expression(lm_eqn(plot[plot$lab == i & plot$sample == s,]))), ", zeroes: ", missing[missing$lab == i & missing$sample == s, "zeroes"])
            index = index + 1
        }
    }
}

pdf(gsub(".tsv", "_zeroes.pdf", args[1]), bg = "white", width = 70, height = 45)
#pdf(gsub(".tsv", ".pdf", args[1]), bg = "white", width = 70, height = 45)
ggplot(plot, aes(x=conc, y=count, color="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 = 30, colour = "black"), axis.text.y = element_text(size = 30,  colour = "black"),
       plot.title = element_text(size = 30), axis.title.x = element_text(size = 18), axis.title.y = element_text(size = 18),
       legend.position = "none", strip.text.x=element_text(size=40), strip.text.y=element_text(size=40)) + ggtitle(unique(plot$category)) +
       facet_grid( sample ~ lab, scales = "free") + 
#       geom_smooth(data=finalE,method=lm,se=FALSE,fullrange=TRUE, size=1.5) +
       geom_smooth(method=lm,se=FALSE,fullrange=TRUE, size=1.5) + 
       theme(legend.position = "none") +
       geom_text(data = graphLabels, aes(x = 1, y = 5, label = label), size = 12)
dev.off()