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library(ggplot2)
library(reshape2)
library(scales)

args <- commandArgs(trailingOnly = TRUE)

input.file = args[1] #the data that's get turned into the "SHM overview" table in the html report "data_sum.txt"

plot1.path = args[2]
plot1.png = paste(plot1.path, ".png", sep="")
plot1.txt = paste(plot1.path, ".txt", sep="")

plot2.path = args[3]
plot2.png = paste(plot2.path, ".png", sep="")
plot2.txt = paste(plot2.path, ".txt", sep="")

plot3.path = args[4]
plot3.png = paste(plot3.path, ".png", sep="")
plot3.txt = paste(plot3.path, ".txt", sep="")

dat = read.table(input.file, header=F, sep=",", quote="", stringsAsFactors=F, fill=T, row.names=1)



classes = c("ca", "ca1", "ca2", "cg", "cg1", "cg2", "cg3", "cg4", "cm")
xyz = c("x", "y", "z")
new.names = c(paste(rep(classes, each=3), xyz, sep="."), paste("un", xyz, sep="."), paste("all", xyz, sep="."))

names(dat) = new.names

dat["RGYW.WRCY",] = colSums(dat[c(13,14),])
dat["TW.WA",] = colSums(dat[c(15,16),])

data1 = dat[c("RGYW.WRCY", "TW.WA"),]

data1 = data1[,names(data1)[grepl(".z", names(data1))]]
names(data1) = gsub("\\..*", "", names(data1))

data1 = melt(t(data1))

names(data1) = c("Class", "Type", "value")

write.table(data1, plot1.txt, quote=F, sep="\t", na="", row.names=F, col.names=T)

p = ggplot(data1, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge") + ylab("% of mutations") + guides(fill=guide_legend(title=NULL))
png(filename=plot1.png)
print(p)
dev.off()

data2 = dat[5:8,]

data2["sum",] = colSums(data2)

data2 = data2[,names(data2)[grepl("\\.x", names(data2))]]
names(data2) = gsub(".x", "", names(data2))

data2["A/T",] = round(colSums(data2[3:4,]) / data2["sum",] * 100, 1)
data2["A/T",is.nan(unlist(data2["A/T",]))] = 0

data2["G/C transversions",] = round(data2[2,] / data2["sum",] * 100, 1)
data2["G/C transitions",] = round(data2[1,] / data2["sum",] * 100, 1)


data2["G/C transversions",is.nan(unlist(data2["G/C transversions",]))] = 0
data2["G/C transversions",is.infinite(unlist(data2["G/C transversions",]))] = 0
data2["G/C transitions",is.nan(unlist(data2["G/C transitions",]))] = 0
data2["G/C transitions",is.infinite(unlist(data2["G/C transitions",]))] = 0

data2 = melt(t(data2[6:8,]))

names(data2) = c("Class", "Type", "value")

write.table(data2, plot2.txt, quote=F, sep="\t", na="", row.names=F, col.names=T)

p = ggplot(data2, aes(x=Class, y=value, fill=Type)) + geom_bar(position="fill", stat="identity") + scale_y_continuous(labels=percent_format()) + guides(fill=guide_legend(title=NULL)) + ylab("% of mutations")
png(filename=plot2.png)
print(p)
dev.off()

data3 = dat[c(5, 6, 8, 17:20),]
data3 = data3[,names(data3)[grepl("\\.x", names(data3))]]
names(data3) = gsub(".x", "", names(data3))

data3["G/C transitions",] = round(data3[1,] / (data3[5,] + data3[7,]) * 100, 1)

data3["G/C transversions",] = round(data3[2,] / (data3[5,] + data3[7,]) * 100, 1)

data3["A/T",] = round(data3[3,] / (data3[4,] + data3[6,]) * 100, 1)

data3["G/C transitions",is.nan(unlist(data3["G/C transitions",]))] = 0
data3["G/C transitions",is.infinite(unlist(data3["G/C transitions",]))] = 0

data3["G/C transversions",is.nan(unlist(data3["G/C transversions",]))] = 0
data3["G/C transversions",is.infinite(unlist(data3["G/C transversions",]))] = 0

data3["A/T",is.nan(unlist(data3["A/T",]))] = 0
data3["A/T",is.infinite(unlist(data3["A/T",]))] = 0

data3 = melt(t(data3[8:10,]))
names(data3) = c("Class", "Type", "value")

write.table(data3, plot3.txt, quote=F, sep="\t", na="", row.names=F, col.names=T)

p = ggplot(data3, aes(Class, value)) + geom_bar(aes(fill=Type), stat="identity", position="dodge") + ylab("% of nucleotides") + guides(fill=guide_legend(title=NULL))
png(filename=plot3.png)
print(p)
dev.off()