# R script for Peak Model
#  -- generated by MACS
p <- c(0.0478541357483,0.0559520374671,0.0635717166436,0.0716696183625,0.0797037570757,0.07963999407,0.0800544536068,0.080213861121,0.0799906906012,0.0801500981153,0.0800863351097,0.0803095056295,0.0806602021606,0.0803732686351,0.0803413871323,0.080405150138,0.0799588090983,0.080022572104,0.0801500981153,0.080213861121,0.0804370316408,0.0797994015842,0.0797675200814,0.0800863351097,0.0803732686351,0.080213861121,0.080405150138,0.0807558466691,0.0810108986917,0.0807877281719,0.0809471356861,0.0816166472455,0.0816485287483,0.0814891212342,0.0813615952229,0.0810427801946,0.0807558466691,0.0803095056295,0.0799269275955,0.0801182166125,0.0801182166125,0.0794805865559,0.0795443495615,0.0795443495615,0.0795443495615,0.0795762310644,0.0795762310644,0.0794805865559,0.0794487050531,0.0792574160361,0.0789067195049,0.0790661270191,0.0785879044766,0.078715430488,0.0785879044766,0.0788429564993,0.0784603784653,0.0784284969625,0.0782690894483,0.0784284969625,0.0785879044766,0.0789386010078,0.0792892975389,0.0792255345332,0.0794168235502,0.0793530605446,0.0797356385785,0.079831283087,0.0798631645899,0.0796081125672,0.0794168235502,0.0789067195049,0.0784603784653,0.0782690894483,0.0779183929172,0.0782372079455,0.0779821559229,0.0776314593917,0.0778227484087,0.078141563437,0.0780459189285,0.0782690894483,0.0784603784653,0.0787473119908,0.0791617715276,0.0787473119908,0.0791298900248,0.07963999407,0.0792892975389,0.0790661270191,0.0794168235502,0.0794168235502,0.0797994015842,0.0796081125672,0.0792574160361,0.0792574160361,0.0790023640134,0.0786516674823,0.0789067195049,0.0790023640134,0.0789386010078,0.0790023640134,0.0788748380021,0.0788429564993,0.0790980085219,0.0793849420474,0.079831283087,0.0798631645899,0.080022572104,0.0802776241266,0.0805007946465,0.0809790171889,0.0810746616974,0.0810427801946,0.0806920836634,0.0805007946465,0.0803413871323,0.0806283206578,0.080213861121,0.079831283087,0.0797675200814,0.0792255345332,0.0793211790417,0.0790023640134,0.0789386010078,0.0787791934936,0.0785560229738,0.078715430488,0.0793530605446,0.0795762310644,0.0797675200814,0.0798950460927,0.080022572104,0.0808196096748,0.0810427801946,0.0812659507144,0.0816804102512,0.0816485287483,0.0814253582285,0.081521002737,0.0814572397314,0.081903580771,0.0817760547597,0.0816166472455,0.0817441732568,0.081903580771,0.0819992252795,0.0819354622738,0.0823180403078,0.0821267512908,0.0819354622738,0.0814891212342,0.0812340692116,0.0811703062059,0.0811703062059,0.08132971372,0.0811384247031,0.0810108986917,0.0804370316408,0.0805645576521,0.0804370316408,0.0803732686351,0.080405150138,0.0805326761493,0.0803095056295,0.080022572104,0.0799906906012,0.0799906906012,0.0800863351097,0.0801182166125,0.0805007946465,0.0799588090983,0.0803095056295,0.0799588090983,0.079831283087,0.0797994015842,0.07963999407,0.0797037570757,0.0797675200814,0.0795762310644,0.0789704825106,0.0794168235502,0.0791617715276,0.0792892975389,0.0793530605446,0.0791936530304,0.0791298900248,0.0789067195049,0.0789704825106,0.0792255345332,0.0794487050531,0.0797356385785,0.0803095056295,0.0803095056295,0.0805645576521,0.0809471356861,0.0811384247031,0.0813615952229,0.08132971372,0.0814891212342,0.0818079362625,0.0817441732568,0.0812659507144,0.0815528842399,0.0813615952229,0.0817441732568,0.081903580771,0.082094869788,0.0816485287483,0.0812340692116,0.0811065432002,0.0809790171889,0.0811703062059,0.0811065432002,0.0811065432002,0.0807558466691,0.0804689131436,0.080405150138,0.0807877281719,0.0808833726804,0.0809152541833,0.0810427801946,0.0809790171889,0.0810746616974,0.0812340692116,0.0806920836634,0.0807558466691,0.0808514911776,0.0809790171889,0.0811065432002,0.081521002737,0.0816485287483,0.0816804102512,0.0815528842399,0.0818716992682,0.0821267512908,0.0823818033134,0.0825412108276,0.0826049738333,0.0828919073587,0.0821586327936,0.0818398177653,0.0814572397314,0.0816166472455,0.0814572397314,0.0814572397314,0.0816804102512,0.0815528842399,0.0816166472455,0.0813934767257,0.0819673437767,0.0824455663191,0.0831469593814,0.0828919073587,0.0831788408842,0.0837208264323,0.0834338929068,0.0830831963757,0.0831469593814,0.083593300421,0.0834657744097,0.0830831963757,0.0827962628502,0.0829237888616,0.0824136848163,0.0824455663191,0.0823499218106,0.0828281443531,0.0830194333701,0.0827324998446,0.0825412108276,0.0825093293248,0.0826049738333,0.0827643813474,0.0833063668955,0.0829237888616,0.0833063668955,0.0830831963757,0.0826368553361,0.0828600258559,0.0831788408842,0.0835295374153,0.0833701299012,0.0832426038899,0.0830513148729,0.0833063668955,0.0831150778785,0.0830831963757,0.0832426038899,0.0830831963757,0.0826368553361,0.0827962628502,0.0829875518672,0.0827643813474,0.0826049738333,0.0827006183417,0.0827006183417,0.0830194333701,0.0829237888616,0.0825730923304,0.0829237888616,0.0827006183417,0.0826368553361,0.0829237888616,0.0832744853927,0.0832744853927,0.0831788408842,0.083210722387,0.0835295374153,0.0842309304776,0.0845497455059,0.0845816270087,0.0848047975285,0.0848366790314,0.084836679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m <- 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ycorr <- 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altd  <- c(0, 39, 92, 119, 140, 164, 209, 256, 532, 549, 570, 594)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('36-JAG-GSE51537/JAG-GFP-replicate-2-GSM1247500/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) : 0,39,92,119,140,164,209,256,532,549,570,594',bty='n')
dev.off()