# R script for Peak Model
#  -- generated by MACS
p <- c(0.0458962251001,0.0539718915079,0.0619613408365,0.0698070950334,0.0773941979929,0.0773079809138,0.0772505028611,0.0771068077293,0.0772217638348,0.077164285782,0.077164285782,0.0765607662284,0.0758710295957,0.0754399442003,0.0753249880949,0.0748939026994,0.0749513807522,0.0750375978312,0.0747502075676,0.0749801197785,0.0751525539367,0.0753537271212,0.0755549003058,0.0755549003058,0.0758997686221,0.0759285076485,0.075497422253,0.0752387710158,0.075497422253,0.075181292963,0.0750088588049,0.074778946594,0.0749801197785,0.0754399442003,0.0752387710158,0.0753537271212,0.0755836393321,0.075813551543,0.0754399442003,0.0752962490685,0.0753537271212,0.0752675100421,0.0750375978312,0.0746927295149,0.0742329050931,0.0742041660667,0.0744053392513,0.0744053392513,0.0742616441195,0.0740317319086,0.0737156026186,0.0738880367768,0.0738018196977,0.0739455148295,0.0743478611985,0.0744915563304,0.0747502075676,0.0742903831458,0.0742329050931,0.0746639904885,0.0751525539367,0.0750663368576,0.075181292963,0.0750088588049,0.0752675100421,0.0748651636731,0.0746639904885,0.0749513807522,0.0752675100421,0.0753249880949,0.0754112051739,0.075497422253,0.0759572466748,0.0762446369384,0.0760434637539,0.0764745491493,0.076445810123,0.0767906784393,0.0769343735711,0.0767332003866,0.0765607662284,0.076761939413,0.0763308540175,0.0763308540175,0.0762446369384,0.0761584198594,0.0759285076485,0.075813551543,0.0755261612794,0.0755836393321,0.0757848125167,0.0754112051739,0.0756698564112,0.0756411173848,0.0753249880949,0.0750375978312,0.0752675100421,0.075497422253,0.0757273344639,0.0757560734903,0.0757848125167,0.0766182442811,0.0758997686221,0.0757273344639,0.0761009418066,0.0765607662284,0.0762733759648,0.0754686832267,0.0751525539367,0.0756123783585,0.0754399442003,0.074462817304,0.0748939026994,0.0748364246467,0.0749226417258,0.0753249880949,0.0754686832267,0.0758710295957,0.0761009418066,0.0759285076485,0.0759572466748,0.0765320272021,0.0762446369384,0.0762446369384,0.0764170710966,0.0759572466748,0.0761009418066,0.0759572466748,0.0757560734903,0.0753249880949,0.0752962490685,0.0748939026994,0.0752387710158,0.074778946594,0.0744053392513,0.0745490343831,0.0746352514622,0.0745490343831,0.0746927295149,0.0748076856203,0.0745490343831,0.0741754270404,0.0744053392513,0.0749513807522,0.074778946594,0.074462817304,0.0742903831458,0.0743766002249,0.0747214685413,0.0745777734094,0.0746639904885,0.0750088588049,0.0742616441195,0.0744340782776,0.0744340782776,0.0746927295149,0.074462817304,0.0745777734094,0.0742903831458,0.0741754270404,0.0743478611985,0.0743191221722,0.0748939026994,0.074778946594,0.0747502075676,0.0750375978312,0.075497422253,0.0752675100421,0.0754399442003,0.0757560734903,0.0758422905694,0.0761584198594,0.0762158979121,0.0764745491493,0.0769343735711,0.0773654589666,0.0773367199402,0.0779115004674,0.0779115004674,0.0782276297574,0.0784862809947,0.078515020021,0.0786012371001,0.078112673652,0.077796544362,0.0774516760456,0.0775378931247,0.0775666321511,0.0773654589666,0.0771068077293,0.0767332003866,0.0765607662284,0.0760722027803,0.0760434637539,0.0760434637539,0.075497422253,0.0751525539367,0.074778946594,0.0752387710158,0.0753824661476,0.0756985954376,0.0760147247275,0.0765607662284,0.0770493296766,0.0771068077293,0.0771930248084,0.0775091540984,0.0776241102038,0.077480415072,0.0780264565729,0.0779115004674,0.0776241102038,0.0773367199402,0.0774229370193,0.0777103272829,0.077480415072,0.0773654589666,0.0778540224147,0.0775666321511,0.0771355467557,0.076848156492,0.0770205906502,0.0770493296766,0.0765320272021,0.0770493296766,0.0772505028611,0.0773654589666,0.076761939413,0.0773079809138,0.0773941979929,0.077796544362,0.0780264565729,0.0787736712583,0.0786299761265,0.0776815882565,0.0781414126783,0.0783713248892,0.077796544362,0.0773079809138,0.077164285782,0.0768768955184,0.0769631125975,0.076848156492,0.0772217638348,0.0776241102038,0.0771930248084,0.0769056345448,0.0775666321511,0.0776528492302,0.0775953711775,0.0776241102038,0.0775378931247,0.0775091540984,0.0776815882565,0.0775953711775,0.0779977175465,0.0783138468365,0.0786012371001,0.0787449322319,0.0788598883374,0.079147278601,0.0795496249701,0.0789461054165,0.0781414126783,0.0779402394938,0.0779689785202,0.0778540224147,0.0775953711775,0.0774229370193,0.0771930248084,0.0770205906502,0.0761584198594,0.0762446369384,0.0771068077293,0.0775091540984,0.0773941979929,0.0775091540984,0.0772505028611,0.0775953711775,0.0775953711775,0.0780551955993,0.0783138468365,0.0787161932056,0.0786587151529,0.078831149311,0.0790323224956,0.0790035834692,0.079779537181,0.079779537181,0.080095666471,0.0803543177082,0.0806129689455,0.0806704469982,0.0812164884991,0.0809865762882,0.0810440543409,0.0809578372618,0.0806417079718,0.0813601836309,0.0819062251318,0.0820786592899,0.0823947885799,0.082797134949,0.0829983081335,0.0836018276871,0.0842053472407,0.0846939106889,0.0850100399789,0.0846076936098,0.0845789545834,0.0848376058207,0.0847513887416,0.0849525619261,0.0847513887416,0.08472264971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m <- 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ycorr <- 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altd  <- c(2, 124)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('02-AP1-GSE45939-GSE45938/AG-GFP-AP1-GR-ap1-cal-Rep2-GSM1120015/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) : 2,124',bty='n')
dev.off()