# R script for Peak Model
#  -- generated by MACS
p <- c(0.0482716471405,0.0559371018366,0.0638689236843,0.0716527637812,0.0796733746794,0.0794957965784,0.0793182184773,0.0796733746794,0.0796733746794,0.079939741831,0.0801765126325,0.0807092469357,0.0809164213869,0.0809460177371,0.0809164213869,0.0809756140873,0.0813307702894,0.0809756140873,0.0811235958382,0.0810348067876,0.0806796505855,0.0806796505855,0.080590861535,0.0805316688346,0.0806204578851,0.0803244943834,0.0803540907335,0.0804428797841,0.0802948980332,0.0802061089826,0.0807092469357,0.0806204578851,0.0806796505855,0.0811531921883,0.0812123848887,0.0819818899933,0.0815379447407,0.0814491556901,0.0816267337912,0.0817747155421,0.0814195593399,0.0813603666396,0.0811531921883,0.0809460177371,0.080768439636,0.0803244943834,0.0803540907335,0.0805020724844,0.0804724761342,0.0806204578851,0.0807980359862,0.0808276323364,0.0810348067876,0.0809164213869,0.0809164213869,0.0809164213869,0.0808868250367,0.0809460177371,0.0809460177371,0.0806796505855,0.0805612651848,0.080590861535,0.0806796505855,0.0809164213869,0.0807980359862,0.0808276323364,0.081093999488,0.081093999488,0.0807092469357,0.0807092469357,0.0807092469357,0.0806796505855,0.0806500542353,0.0805612651848,0.0806204578851,0.0804724761342,0.0801469162823,0.0796141819791,0.0798509527805,0.07976216373,0.0798213564303,0.0800285308816,0.0797917600801,0.0797029710296,0.0800877235819,0.0801765126325,0.0805316688346,0.0812419812389,0.0810348067876,0.0812123848887,0.0815379447407,0.0813011739392,0.081597137441,0.081922697293,0.0818043118923,0.0820410826937,0.0821298717442,0.0817451191919,0.0820114863435,0.0820114863435,0.0819818899933,0.0819818899933,0.0819522936431,0.0818635045926,0.0818635045926,0.0815379447407,0.0816859264915,0.082100275394,0.0818635045926,0.0818043118923,0.0816563301414,0.082100275394,0.0822778534951,0.082425835246,0.0825442206467,0.082928973199,0.0827217987478,0.0823074498453,0.0828105877983,0.0826330096972,0.0824554315962,0.082425835246,0.0822778534951,0.0821594680944,0.082100275394,0.0820114863435,0.0821594680944,0.0823666425456,0.0820706790439,0.082425835246,0.0823666425456,0.0823370461955,0.0821890644446,0.0821298717442,0.0819522936431,0.0817747155421,0.0816859264915,0.0816563301414,0.0818931009428,0.0818043118923,0.081922697293,0.0813011739392,0.0812123848887,0.0809460177371,0.0810644031378,0.0810644031378,0.0811531921883,0.0809164213869,0.0810052104374,0.0808572286866,0.0808276323364,0.081093999488,0.0812123848887,0.0815083483905,0.0812715775891,0.0811827885385,0.0809164213869,0.0810052104374,0.080590861535,0.0805612651848,0.0804428797841,0.0802061089826,0.0800581272317,0.079939741831,0.0799693381812,0.0800285308816,0.080265301683,0.0803540907335,0.0802948980332,0.0802357053328,0.080265301683,0.0804132834339,0.0802948980332,0.0800285308816,0.0798805491307,0.0796733746794,0.0790518513257,0.0788446768744,0.0788150805243,0.0789038695748,0.0791110440261,0.0790222549755,0.0791998330766,0.0792590257769,0.0793182184773,0.0794070075278,0.0799693381812,0.0803244943834,0.0801469162823,0.0802948980332,0.0804132834339,0.0805316688346,0.0805020724844,0.0804428797841,0.080590861535,0.0803244943834,0.0801173199321,0.07976216373,0.0799989345314,0.0800285308816,0.0796733746794,0.0798213564303,0.0800877235819,0.0804132834339,0.0808868250367,0.0809756140873,0.0811531921883,0.0814195593399,0.0814787520403,0.0814195593399,0.0814787520403,0.0813899629898,0.0814491556901,0.0812123848887,0.0804724761342,0.081093999488,0.0809164213869,0.081093999488,0.0808276323364,0.0805316688346,0.080590861535,0.0810052104374,0.0806204578851,0.0805020724844,0.0807388432858,0.080590861535,0.0804724761342,0.0798213564303,0.0800877235819,0.0801173199321,0.0801469162823,0.0796141819791,0.0796437783293,0.079939741831,0.0797917600801,0.0795845856289,0.0796141819791,0.0795549892787,0.0795549892787,0.079436603878,0.0792886221271,0.0792294294268,0.0793774111777,0.0793774111777,0.0796437783293,0.0798213564303,0.0798805491307,0.0804724761342,0.0807388432858,0.0812715775891,0.0815083483905,0.0816859264915,0.0818339082424,0.0818635045926,0.0822186607948,0.0819522936431,0.0819522936431,0.082100275394,0.0823074498453,0.0821890644446,0.0820114863435,0.082100275394,0.0818931009428,0.0821594680944,0.081597137441,0.081922697293,0.0823370461955,0.0821298717442,0.0819522936431,0.0820706790439,0.0826034133471,0.0824850279464,0.0828401841485,0.0825146242965,0.0826330096972,0.0828993768488,0.0826034133471,0.0828401841485,0.0827217987478,0.0827809914481,0.082425835246,0.082425835246,0.082100275394,0.082100275394,0.0822186607948,0.0818043118923,0.0818043118923,0.0817155228417,0.081922697293,0.0817747155421,0.0819522936431,0.0820706790439,0.0821890644446,0.0826626060474,0.0828401841485,0.0826034133471,0.0827809914481,0.0831361476503,0.0830473585997,0.0833433221015,0.083254533051,0.0837872673542,0.0837280746538,0.0836392856033,0.0836096892531,0.0838168637044,0.0838464600545,0.0836096892531,0.0833433221015,0.0831065513001,0.0835504965528,0.0833137257513,0.0833137257513,0.0834617075022,0.0835800929029,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m <- 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ycorr <- 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altd  <- c(0, 38, 81, 139, 183, 191, 197, 209, 239, 267, 273, 366, 383, 445, 472, 488, 505, 527, 534, 540, 558)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('77-EBS-CLF-GSE101428/EBS-FLAG-GSM2915139/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) : 0,38,81,139,183,191,197,209,239,267,273,366,383,445,472,488,505,527,534,540,558',bty='n')
dev.off()