# R script for Peak Model
#  -- generated by MACS
p <- c(0.0458945719573,0.0536606376557,0.0613461663766,0.069177428676,0.076799678343,0.0766961308003,0.0767191413654,0.0766596974057,0.0768955556973,0.0769607522982,0.0771026507826,0.0770489594642,0.0771045683297,0.0769051434327,0.0771237438005,0.0772368790786,0.0771908579485,0.0771486719126,0.0769837628632,0.0769971856928,0.0770566296525,0.0768744626793,0.0768648749439,0.076866792491,0.0766807904236,0.0765829955223,0.0765753253339,0.0765619025043,0.0764008285491,0.0763049511948,0.0760748455445,0.0762109913876,0.0760671753561,0.0760230717731,0.0758102240466,0.0758083064995,0.0757872134816,0.0757603678223,0.0758888434771,0.0757929661228,0.075952122531,0.0760307419615,0.075908018948,0.07588692593,0.0760921034682,0.0761688053517,0.07613045441,0.0760921034682,0.076220579123,0.0763145389302,0.0762148264817,0.0760537525265,0.0761841457284,0.0761592176162,0.0762033211992,0.0761419596925,0.0761956510109,0.0762991985535,0.076153464975,0.076153464975,0.0761457947866,0.0760690929032,0.076021154226,0.0761227842216,0.0760595051678,0.0760288244144,0.0758830908359,0.0758773381946,0.0758063889524,0.0757661204636,0.0758006363112,0.0759463698897,0.0760326595086,0.0759502049839,0.0757411923515,0.075662572921,0.075752697634,0.0757488625398,0.0756165517909,0.0755475200958,0.0754995814186,0.0754746533065,0.075373023311,0.075284816145,0.0753365899163,0.0751160720014,0.0750719684185,0.0748572031448,0.0750086893646,0.075039370118,0.0750412876651,0.0748974716336,0.0748341925798,0.0749089769161,0.0748361101269,0.0749319874812,0.0749032242749,0.0749434927637,0.0749166471045,0.0748955540865,0.0747191397546,0.0748648733332,0.0748821312569,0.0748782961628,0.0750642982301,0.0749665033287,0.0749032242749,0.074816934656,0.0748476154094,0.0749703384229,0.0748265223914,0.0745427254227,0.0746251799474,0.0745791588173,0.0743989093913,0.074483281463,0.0745906640999,0.0744334252388,0.0742608460011,0.0738524084717,0.0739003471489,0.0740825141221,0.0739789665794,0.0739885543148,0.0740192350682,0.0740153999741,0.0736338081039,0.0740441631803,0.0742646810952,0.0746750361716,0.0748073469206,0.0746539431537,0.0746424378712,0.0747133871134,0.0748188522031,0.0747114695663,0.0749703384229,0.0747574906963,0.0744353427859,0.0742991969428,0.074126617705,0.0740786790279,0.0740671737454,0.0738984296018,0.0740038946915,0.0741304527992,0.0739981420503,0.0737852943237,0.0737316030053,0.073656818669,0.0739425331848,0.073946368279,0.0739003471489,0.0739636262027,0.0739789665794,0.0740614211041,0.0741898967589,0.0745734061761,0.0746712010775,0.0747479029609,0.0746462729654,0.074705716925,0.0748130995618,0.0747440678667,0.0745120446693,0.0743317952432,0.0743835690146,0.0741112773284,0.0740978544988,0.0739080173372,0.0738543260188,0.0739617086556,0.0738121399829,0.0737220152699,0.0736683239515,0.0737718714941,0.0738850067722,0.0740307403507,0.0740211526153,0.0741323703463,0.0743433005258,0.074349053167,0.0742915267544,0.0743528882612,0.0742838565661,0.0743854865617,0.0743068671311,0.0742071546827,0.074281939019,0.0744756112747,0.0743375478845,0.074237835436,0.0744238375034,0.0744698586334,0.0746270974945,0.0745734061761,0.0745293025931,0.0744967042926,0.0744545182568,0.0744775288218,0.0743835690146,0.0744104146738,0.0743471356199,0.0742934443015,0.0742071546827,0.0741649686468,0.0738926769605,0.0741457931759,0.0742896092074,0.0741803090235,0.0741496282701,0.0741170299696,0.0739617086556,0.0740863492162,0.0740269052566,0.0741151124225,0.0741822265705,0.0738543260188,0.0736491484806,0.0734919096196,0.0736606537631,0.0737009222519,0.0737220152699,0.0736472309335,0.0736874994223,0.0736031273506,0.0739080173372,0.0741515458172,0.0742723512836,0.0742991969428,0.0740211526153,0.0740652561983,0.0741822265705,0.0742665986423,0.0742320827948,0.0742167424181,0.0740518333687,0.0741803090235,0.0741898967589,0.0741553809113,0.0742953618486,0.074237835436,0.0742876916603,0.0743854865617,0.0744775288218,0.0745695710819,0.0744065795796,0.0740863492162,0.0740556684629,0.074036492992,0.0740153999741,0.0740940194046,0.0740652561983,0.0740096473328,0.0740882667633,0.0740499158216,0.0742244126064,0.0745369727815,0.0744257550505,0.0746577782479,0.0748226872973,0.0746712010775,0.0747459854138,0.0747440678667,0.0748495329565,0.0749223997457,0.0751333299252,0.0751179895485,0.0753998689702,0.0753480951988,0.0753116618042,0.0756472325443,0.0758351521587,0.0760556700736,0.0759252768717,0.0762512598764,0.0762550949705,0.0761726404458,0.0762781055356,0.0764449321321,0.0766577798586,0.0765408094864,0.0767133887241,0.0766692851411,0.0767709151367,0.0766079236344,0.0766251815582,0.0767613274013,0.0767862555134,0.07704512437,0.0770086909754,0.0772215387019,0.0769914330516,0.0770949805942,0.0773212511504,0.0774228811459,0.077401788128,0.0775168409532,0.0776299762312,0.0778102256573,0.0780882699848,0.0783260458235,0.0787479061824,0.0786750393931,0.0791946946534,0.0794804091693,0.0798562483981,0.0804947915778,0.0810010240085,0.0810834785332,0.0815609477576,0.0818255692555,0.0819847256636,0.0827344865743,0.0826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m <- 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ycorr <- 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altd  <- c(4, 193)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('L2600-7x_TetO-2hrs-H3K4me3.2x36mers.hg38-male+opJS5_7x_TetO_b2.unique.dedup.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) : 4,193',bty='n')
dev.off()