# R script for Peak Model
#  -- generated by MACS
p <- c(0.0482822029778,0.0562490071581,0.0642158113384,0.0722307533083,0.0801494196989,0.0800772130145,0.0801494196989,0.0800772130145,0.0800772130145,0.0801494196989,0.0800290752249,0.0801494196989,0.080269764173,0.0801494196989,0.0802216263834,0.0800290752249,0.0798365240665,0.0799809374353,0.0800050063301,0.0800290752249,0.0801734885938,0.0801253508041,0.0799568685405,0.0801734885938,0.0801734885938,0.0804382464366,0.0803660397522,0.0801734885938,0.0799568685405,0.0797402484873,0.0797161795925,0.0797883862769,0.0799809374353,0.0800050063301,0.0801012819093,0.0801734885938,0.0804382464366,0.080630797595,0.0808474176483,0.0810640377015,0.0811362443859,0.0811121754911,0.0810881065963,0.0808955554379,0.0807752109639,0.0806789353846,0.0805345220158,0.080510453121,0.0804623153314,0.080269764173,0.080269764173,0.0802938330678,0.0801253508041,0.0802456952782,0.0802216263834,0.0799568685405,0.0799568685405,0.0798124551717,0.0798605929613,0.0800290752249,0.0799327996457,0.0797643173821,0.0797161795925,0.0796439729081,0.0797161795925,0.0798846618561,0.0799087307509,0.0799809374353,0.0798605929613,0.0797883862769,0.0798365240665,0.0799087307509,0.0801253508041,0.0800772130145,0.0801253508041,0.0801494196989,0.0801734885938,0.0801734885938,0.0801975574886,0.0801494196989,0.0801253508041,0.0801975574886,0.0801975574886,0.0803660397522,0.0804382464366,0.080510453121,0.0804863842262,0.0804863842262,0.0804141775418,0.0804623153314,0.0804863842262,0.0804382464366,0.080390108647,0.0801734885938,0.0801253508041,0.0801734885938,0.0801734885938,0.0801012819093,0.0800290752249,0.0800772130145,0.0799809374353,0.0799087307509,0.0799327996457,0.0800290752249,0.0799087307509,0.0799087307509,0.0799087307509,0.0800772130145,0.080269764173,0.0801975574886,0.0803419708574,0.0804863842262,0.0805585909106,0.080630797595,0.0805826598054,0.0805826598054,0.0807270731743,0.0807752109639,0.0807511420691,0.0807030042794,0.0805826598054,0.0805345220158,0.0804623153314,0.0805826598054,0.0807511420691,0.0806548664898,0.0807030042794,0.0807030042794,0.0807270731743,0.0808714865431,0.0809918310171,0.0810158999119,0.0809918310171,0.0807030042794,0.0804863842262,0.080390108647,0.0800290752249,0.0797643173821,0.0795717662236,0.0794273528548,0.0790422505379,0.0788737682743,0.0786812171159,0.0785849415367,0.0785608726419,0.0784645970626,0.078536803747,0.0784405281678,0.0783442525886,0.0782479770094,0.0783683214834,0.0782720459042,0.0782479770094,0.0785127348522,0.0785608726419,0.0786571482211,0.0786330793263,0.0787293549055,0.0788496993795,0.0788256304847,0.0789941127483,0.0791866639068,0.0792348016964,0.0790903883275,0.079162595012,0.0792588705912,0.0793310772756,0.07940328396,0.0794754906444,0.0796439729081,0.0796439729081,0.0794754906444,0.0795476973288,0.0795717662236,0.0794754906444,0.0793310772756,0.0792348016964,0.0791385261172,0.0790663194327,0.0789941127483,0.0789219060639,0.0789941127483,0.0788978371691,0.0788737682743,0.0789219060639,0.0789941127483,0.0789941127483,0.0791144572224,0.079162595012,0.0790903883275,0.0790181816431,0.0788496993795,0.0789700438535,0.0789459749587,0.0788015615899,0.0788256304847,0.0788496993795,0.0788256304847,0.0788737682743,0.0789941127483,0.0792348016964,0.0795717662236,0.0797643173821,0.0798846618561,0.0801494196989,0.0800290752249,0.0800290752249,0.0799087307509,0.0798846618561,0.0799087307509,0.0796439729081,0.0794754906444,0.0793310772756,0.0793070083808,0.0791866639068,0.0793551461704,0.0794273528548,0.0794754906444,0.0793551461704,0.0793310772756,0.0795958351184,0.0795476973288,0.0794514217496,0.07940328396,0.079523628434,0.0795717662236,0.079523628434,0.0795958351184,0.0798846618561,0.0799809374353,0.0800050063301,0.0802216263834,0.0802216263834,0.0803419708574,0.0802216263834,0.0800531441197,0.0800531441197,0.0800531441197,0.0798365240665,0.0796680418029,0.0795958351184,0.0794995595392,0.0795476973288,0.079523628434,0.0795476973288,0.0796680418029,0.0796439729081,0.0797883862769,0.0799809374353,0.0801253508041,0.080269764173,0.0804623153314,0.0807030042794,0.0807752109639,0.0810640377015,0.08125658886,0.0814250711236,0.0815694844924,0.0816657600716,0.0818583112301,0.0819064490197,0.0820027245989,0.0820027245989,0.0820990001781,0.0819786557041,0.0819305179145,0.0821712068625,0.0820749312833,0.0820027245989,0.0819064490197,0.0817620356508,0.0816416911768,0.0815454155976,0.0814250711236,0.0814010022288,0.0814010022288,0.0811603132807,0.0812325199651,0.0812084510703,0.0811362443859,0.0812325199651,0.0811603132807,0.0810881065963,0.0810399688067,0.0809436932275,0.0809196243327,0.0808955554379,0.0806789353846,0.0807511420691,0.0807992798587,0.0806067287002,0.0804863842262,0.080630797595,0.0807752109639,0.0809677621223,0.0809918310171,0.0812806577548,0.0815213467028,0.0815694844924,0.0816657600716,0.0819305179145,0.0823878269158,0.0824359647054,0.0825081713898,0.0826766536534,0.0829414114963,0.0830858248651,0.0832783760235,0.0834468582872,0.0836875472352,0.0839041672884,0.0839523050781,0.0840245117625,0.084096718446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m <- 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ycorr <- 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altd  <- c(0, 34, 452, 483, 532, 551, 592)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('39-PhyA-GSE48770/PhyA-GFP_2-GSM1184361/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) : 0,34,452,483,532,551,592',bty='n')
dev.off()