# R script for Peak Model
#  -- generated by MACS
p <- c(0.048740872961,0.056632948343,0.0645250237249,0.0725876069084,0.0806014735771,0.080382249261,0.0799925171433,0.0799438006286,0.0798707258566,0.0797245763125,0.0796271432831,0.0797732928272,0.0800168754007,0.0800655919154,0.0800899501727,0.0803091744889,0.0804066075183,0.080382249261,0.0802848162316,0.0803578910036,0.0801386666875,0.080041233658,0.0798463675992,0.0797732928272,0.0797976510845,0.0794566354816,0.0793835607095,0.0793835607095,0.0793104859375,0.0791886946507,0.079554068511,0.0797976510845,0.0799194423713,0.0799194423713,0.0798950841139,0.0800655919154,0.0800899501727,0.0799925171433,0.0802117414595,0.0804066075183,0.079968158886,0.0797489345698,0.0797245763125,0.0796271432831,0.0795297102537,0.0796271432831,0.0797976510845,0.0798950841139,0.0797976510845,0.0798707258566,0.0800168754007,0.080041233658,0.0801386666875,0.0800168754007,0.0801386666875,0.080041233658,0.0800168754007,0.0799438006286,0.0797245763125,0.079480993739,0.0795053519963,0.0795297102537,0.0792617694228,0.0793835607095,0.0792617694228,0.0792861276801,0.0792374111654,0.0792861276801,0.0796515015404,0.0797245763125,0.0795053519963,0.0794322772242,0.0792861276801,0.0792617694228,0.0794566354816,0.0793835607095,0.0792130529081,0.0790912616213,0.0787746042758,0.0786284547316,0.0787989625331,0.078652812989,0.0788720373052,0.0789938285919,0.0788963955625,0.0789207538199,0.0792374111654,0.0794566354816,0.0797245763125,0.0801143084301,0.0802360997169,0.0804309657757,0.0802848162316,0.0802360997169,0.0802848162316,0.080382249261,0.0802848162316,0.0801630249448,0.0802117414595,0.079968158886,0.080041233658,0.0800168754007,0.0801873832022,0.0801873832022,0.0800655919154,0.0799194423713,0.0801630249448,0.0802360997169,0.0802604579742,0.0805040405477,0.0805283988051,0.0807476231212,0.0809668474374,0.081283504783,0.0815027290992,0.0817950281874,0.0817219534153,0.0817950281874,0.08177066993,0.0818437447021,0.081697595158,0.0816001621286,0.0815270873565,0.0814296543271,0.0814540125845,0.0814783708418,0.0814296543271,0.0816245203859,0.0816001621286,0.0816001621286,0.0818193864447,0.0819411777315,0.0819655359888,0.08177066993,0.0816488786433,0.0816488786433,0.0815270873565,0.0812347882683,0.0810642804668,0.0809668474374,0.080869414408,0.0805527570624,0.0805040405477,0.080455324033,0.0802848162316,0.0798463675992,0.0796758597978,0.0795784267684,0.0796515015404,0.0793348441948,0.0793835607095,0.0795784267684,0.0796027850257,0.0797002180551,0.0797245763125,0.0798950841139,0.0800899501727,0.0802848162316,0.0802848162316,0.080382249261,0.0802360997169,0.0802848162316,0.0800655919154,0.0798950841139,0.0798220093419,0.0798707258566,0.0797002180551,0.079480993739,0.0793104859375,0.0792861276801,0.0791886946507,0.0789451120772,0.0788963955625,0.0788476790478,0.0788963955625,0.0787989625331,0.0788233207905,0.0788720373052,0.0789451120772,0.079066903364,0.0790425451066,0.0789207538199,0.0788963955625,0.0789938285919,0.0788963955625,0.0789694703346,0.0788963955625,0.0787502460184,0.078725887761,0.0785066634449,0.0785310217022,0.078725887761,0.0787989625331,0.0785797382169,0.078652812989,0.0786284547316,0.078725887761,0.0788963955625,0.0787746042758,0.0789938285919,0.0788963955625,0.0786771712463,0.0788720373052,0.0789694703346,0.0789451120772,0.0789451120772,0.0787746042758,0.078652812989,0.0787502460184,0.0785066634449,0.0785066634449,0.0786771712463,0.078652812989,0.0785310217022,0.0784335886728,0.0781412895846,0.0780682148125,0.0781412895846,0.0781169313273,0.0779951400405,0.0778977070111,0.0779464235258,0.0778002739817,0.0779220652684,0.0779464235258,0.0781412895846,0.0780925730699,0.0778977070111,0.077824632239,0.0779464235258,0.0779707817831,0.0778489904964,0.0776784826949,0.0776297661802,0.0775323331508,0.0774349001214,0.077410541864,0.0775079748935,0.0775810496655,0.0776297661802,0.0778977070111,0.0778002739817,0.0779220652684,0.0781412895846,0.0784823051875,0.0787502460184,0.0791156198787,0.0794566354816,0.0795784267684,0.0797976510845,0.0800168754007,0.0803335327463,0.0805040405477,0.0805040405477,0.0805040405477,0.0806014735771,0.0806745483492,0.0805283988051,0.0805771153198,0.0806014735771,0.0804066075183,0.0803091744889,0.080382249261,0.0806014735771,0.0807232648639,0.0806258318345,0.0805527570624,0.0806258318345,0.0807476231212,0.0806745483492,0.0806258318345,0.0806989066065,0.0807232648639,0.0805040405477,0.0802848162316,0.0802604579742,0.0803091744889,0.0803091744889,0.0801630249448,0.0802117414595,0.0802604579742,0.0800899501727,0.0800168754007,0.0801873832022,0.0804066075183,0.0805040405477,0.0805040405477,0.0805283988051,0.0807232648639,0.080796339636,0.0809668474374,0.0810886387242,0.0812104300109,0.081283504783,0.0814540125845,0.0816488786433,0.0818437447021,0.0820142525035,0.0821604020477,0.0821116855329,0.0822091185624,0.0825014176506,0.0827450002241,0.0827206419667,0.0826232089373,0.0825257759079,0.0826232089373,0.082671925452,0.0826475671947,0.0828911497682,0.0828424332535,0.0829885827976,0.0829642245403,0.0832078071138,0.083451389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m <- 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ycorr <- 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altd  <- c(1, 34, 508, 524, 594)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('39-PhyA-GSE48770/PhyA-GFP_3-GSM1184362/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) : 1,34,508,524,594',bty='n')
dev.off()