# R script for Peak Model
#  -- generated by MACS
p <- c(0.0496778466912,0.0526886252785,0.0594628771,0.068495212862,0.0737640753899,0.0775275486241,0.0722586860962,0.0707532968026,0.0715059914494,0.0647317396279,0.0632263503342,0.0654844342747,0.0647317396279,0.0602155717469,0.0609682663937,0.0564520985127,0.0609682663937,0.0617209610405,0.0609682663937,0.068495212862,0.0692479075089,0.0700006021557,0.0737640753899,0.0790329379177,0.0827964111519,0.0858071897393,0.0812910218583,0.0858071897393,0.0835491057988,0.0820437165051,0.0835491057988,0.0805383272114,0.0782802432709,0.0767748539772,0.0752694646836,0.0775275486241,0.0760221593304,0.0745167700367,0.0760221593304,0.0722586860962,0.0767748539772,0.0843018004456,0.0850544950924,0.0865598843861,0.0820437165051,0.0812910218583,0.0820437165051,0.0820437165051,0.0858071897393,0.0843018004456,0.0745167700367,0.0700006021557,0.0669898235684,0.068495212862,0.0707532968026,0.0647317396279,0.0647317396279,0.0632263503342,0.0579574878063,0.0572047931595,0.0609682663937,0.0602155717469,0.063979044981,0.0564520985127,0.0579574878063,0.0602155717469,0.0602155717469,0.0609682663937,0.0632263503342,0.0632263503342,0.0609682663937,0.0654844342747,0.0602155717469,0.0632263503342,0.0669898235684,0.0722586860962,0.0737640753899,0.0715059914494,0.0722586860962,0.0715059914494,0.0760221593304,0.0745167700367,0.0797856325646,0.0797856325646,0.0782802432709,0.0767748539772,0.0812910218583,0.0873125790329,0.0873125790329,0.091828746914,0.0933341362076,0.0895706629734,0.0910760522671,0.0910760522671,0.0925814415608,0.0873125790329,0.0827964111519,0.0790329379177,0.0797856325646,0.0767748539772,0.0707532968026,0.0730113807431,0.0669898235684,0.0669898235684,0.0609682663937,0.0632263503342,0.0654844342747,0.0677425182152,0.0647317396279,0.068495212862,0.0692479075089,0.0700006021557,0.0722586860962,0.0752694646836,0.0760221593304,0.0767748539772,0.0737640753899,0.0722586860962,0.0745167700367,0.0745167700367,0.0767748539772,0.0752694646836,0.0797856325646,0.0775275486241,0.0775275486241,0.0745167700367,0.0730113807431,0.0752694646836,0.0805383272114,0.0790329379177,0.0812910218583,0.0827964111519,0.0752694646836,0.0745167700367,0.0737640753899,0.0775275486241,0.0835491057988,0.0812910218583,0.0797856325646,0.0790329379177,0.0752694646836,0.0722586860962,0.0767748539772,0.0782802432709,0.0873125790329,0.0865598843861,0.0805383272114,0.0835491057988,0.0752694646836,0.0760221593304,0.0782802432709,0.0820437165051,0.0812910218583,0.0797856325646,0.0722586860962,0.0745167700367,0.0790329379177,0.0752694646836,0.0775275486241,0.0760221593304,0.0745167700367,0.0715059914494,0.068495212862,0.0700006021557,0.0700006021557,0.068495212862,0.068495212862,0.0722586860962,0.0722586860962,0.0715059914494,0.0730113807431,0.0805383272114,0.0797856325646,0.0790329379177,0.0805383272114,0.0827964111519,0.0782802432709,0.0790329379177,0.0805383272114,0.0843018004456,0.0873125790329,0.0797856325646,0.0835491057988,0.0873125790329,0.0865598843861,0.0805383272114,0.0827964111519,0.0782802432709,0.0760221593304,0.0737640753899,0.0692479075089,0.0730113807431,0.0737640753899,0.0692479075089,0.068495212862,0.0692479075089,0.0722586860962,0.0722586860962,0.0767748539772,0.0790329379177,0.0820437165051,0.0767748539772,0.0745167700367,0.0730113807431,0.0700006021557,0.068495212862,0.0654844342747,0.0647317396279,0.0632263503342,0.0617209610405,0.0564520985127,0.0587101824532,0.0594628771,0.0654844342747,0.0692479075089,0.0707532968026,0.068495212862,0.0707532968026,0.0730113807431,0.0745167700367,0.0767748539772,0.0752694646836,0.0767748539772,0.0775275486241,0.0782802432709,0.0805383272114,0.0820437165051,0.0843018004456,0.0782802432709,0.0745167700367,0.0707532968026,0.0767748539772,0.0767748539772,0.0700006021557,0.0722586860962,0.0707532968026,0.0760221593304,0.0715059914494,0.0752694646836,0.0812910218583,0.0865598843861,0.0827964111519,0.0850544950924,0.0873125790329,0.0820437165051,0.0880652736798,0.0820437165051,0.0843018004456,0.0850544950924,0.0805383272114,0.0820437165051,0.0797856325646,0.0775275486241,0.0760221593304,0.0812910218583,0.0767748539772,0.0760221593304,0.0760221593304,0.0737640753899,0.0760221593304,0.0715059914494,0.0752694646836,0.0722586860962,0.0730113807431,0.068495212862,0.0669898235684,0.0707532968026,0.0715059914494,0.0730113807431,0.0707532968026,0.0745167700367,0.0707532968026,0.0715059914494,0.0767748539772,0.0775275486241,0.0775275486241,0.0737640753899,0.0707532968026,0.0715059914494,0.0722586860962,0.0707532968026,0.0722586860962,0.0760221593304,0.0692479075089,0.0737640753899,0.0730113807431,0.0737640753899,0.0820437165051,0.0805383272114,0.0790329379177,0.0812910218583,0.0820437165051,0.0790329379177,0.0797856325646,0.0797856325646,0.0775275486241,0.0797856325646,0.0730113807431,0.0730113807431,0.0737640753899,0.0715059914494,0.068495212862,0.0722586860962,0.0715059914494,0.0707532968026,0.0737640753899,0.0677425182152,0.0707532968026,0.0715059914494,0.0752694646836,0.0745167700367,0.0850544950924,0.0843018004456,0.08580718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m <- 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ycorr <- 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altd  <- c(70, 110, 156, 179, 189, 221, 258, 420, 464, 500, 579)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('03-PolIV-GSE45368/PolIV-ChIP-GSM1103231/all.1x36mers.TAIR10.unique.MACS2_model.pdf',height=6,width=6)
plot(x,p,type='l',col=c('red'),main='Peak Model',xlab='Distance to the middle',ylab='Percentage')
lines(x,m,col=c('blue'))
legend('topleft',c('forward tags','reverse tags'),lty=c(1,1,1),col=c('red','blue'))
plot(xcorr,ycorr,type='l',col=c('black'),main='Cross-Correlation',xlab='Lag between + and - tags',ylab='Correlation')
abline(v=altd,lty=2,col=c('red'))
legend('topleft','alternative lag(s)',lty=2,col='red')
legend('right','alt lag(s) : 70,110,156,179,189,221,258,420,464,500,579',bty='n')
dev.off()