# R script for Peak Model
#  -- generated by MACS
p <- c(0.0461246311186,0.053760648645,0.0614995081582,0.0691612361813,0.0769772271846,0.0770800691715,0.0769000956945,0.0770543586748,0.0771057796682,0.0773885951322,0.0775685686092,0.0777228315896,0.0774914371191,0.0774400161256,0.0773371741387,0.0770800691715,0.0772857531453,0.0772086216551,0.0771057796682,0.0770800691715,0.0769000956945,0.076848674701,0.0773371741387,0.0773628846355,0.0774400161256,0.0777999630797,0.0778513840732,0.077774252583,0.0778770945699,0.0780056470535,0.0787512514584,0.0789826459289,0.0788540934453,0.0794454348699,0.0797025398371,0.0797796713273,0.0798310923207,0.080268170765,0.0805766967257,0.0805252757322,0.0797025398371,0.0797539608306,0.0798310923207,0.0794711453666,0.0795482768568,0.0795996978502,0.0795996978502,0.0792397508961,0.0790083564256,0.0791111984125,0.0792140403994,0.0792911718896,0.0791369089093,0.0791883299027,0.0791883299027,0.0791883299027,0.0793940138765,0.0794711453666,0.0797539608306,0.0797025398371,0.0798825133142,0.0799596448043,0.0802167497716,0.0801653287781,0.0797796713273,0.079805381824,0.079805381824,0.0797539608306,0.0797025398371,0.0797282503339,0.0799339343076,0.079625408347,0.0796511188437,0.0799339343076,0.0800110657978,0.0799596448043,0.079805381824,0.0801910392748,0.0799853553011,0.0799596448043,0.0799339343076,0.0800110657978,0.0798825133142,0.079342592883,0.0794197243732,0.0794197243732,0.0794968558634,0.0793683033797,0.079342592883,0.0796511188437,0.0792140403994,0.0792397508961,0.0790340669224,0.0791369089093,0.0791369089093,0.0786226989748,0.0784941464912,0.0783398835109,0.0784427254978,0.0779285155633,0.078237041524,0.0780056470535,0.0777228315896,0.0776971210928,0.0774914371191,0.0779285155633,0.0780313575502,0.0779285155633,0.0778256735764,0.0780570680469,0.0783655940076,0.0784684359945,0.0792397508961,0.0794711453666,0.0797282503339,0.0795482768568,0.0795739873535,0.0793683033797,0.0797025398371,0.0796768293404,0.0791111984125,0.0793168823863,0.0788283829486,0.078879803942,0.0789826459289,0.0789055144388,0.0788026724519,0.0792397508961,0.0785455674847,0.0784427254978,0.0785198569879,0.0780827785437,0.0784427254978,0.0779028050666,0.0778513840732,0.0780056470535,0.077774252583,0.0775171476158,0.0779028050666,0.077774252583,0.077774252583,0.0780313575502,0.0776457000994,0.0780827785437,0.0776457000994,0.0775428581125,0.077594279106,0.0776971210928,0.0776714105961,0.0774914371191,0.0774400161256,0.0774400161256,0.0775685686092,0.0777485420863,0.0778256735764,0.0779799365568,0.0780313575502,0.0779799365568,0.0781341995371,0.0783655940076,0.0786741199683,0.078879803942,0.0786741199683,0.0783398835109,0.0786226989748,0.0785969884781,0.0788283829486,0.0787512514584,0.0786741199683,0.0788283829486,0.0788283829486,0.0786741199683,0.0789826459289,0.0792911718896,0.0793683033797,0.0794454348699,0.0795482768568,0.0796511188437,0.079625408347,0.0798825133142,0.0798568028175,0.0800110657978,0.0801396182814,0.0802167497716,0.0801139077847,0.0802424602683,0.0801653287781,0.0804738547388,0.0808338016929,0.0808338016929,0.0808852226863,0.0808595121896,0.0806538282158,0.0804481442421,0.0805252757322,0.0803967232486,0.0804481442421,0.0805509862289,0.0802938812617,0.0799853553011,0.0798310923207,0.0795739873535,0.0795996978502,0.0795996978502,0.0795482768568,0.0793168823863,0.079162619406,0.078699830465,0.0789569354322,0.0791883299027,0.0793683033797,0.0797025398371,0.0796768293404,0.0799082238109,0.0801396182814,0.0806281177191,0.0809880646732,0.0811680381503,0.0811680381503,0.0810137751699,0.081193748647,0.0813223011306,0.0814508536142,0.0812708801372,0.0813994326208,0.0811680381503,0.0808080911962,0.0809623541765,0.0808852226863,0.081193748647,0.0811423276535,0.0808852226863,0.080910933183,0.081373722124,0.0813480116273,0.0815022746076,0.0815279851044,0.0814251431175,0.0814765641109,0.0814251431175,0.0816051165945,0.0815536956011,0.0817850900716,0.0817336690781,0.081656537588,0.0819393530519,0.0820421950388,0.0823507209995,0.0822478790126,0.0825306944765,0.0823507209995,0.0827363784503,0.0826335364634,0.0823507209995,0.0822221685159,0.0819393530519,0.0822478790126,0.0822735895093,0.0821964580191,0.0817336690781,0.0816822480847,0.0818879320585,0.0817850900716,0.0820421950388,0.082299300006,0.0823250105027,0.0819650635486,0.0817593795749,0.0820679055355,0.0819650635486,0.0821964580191,0.0820679055355,0.0823764314962,0.0821707475224,0.0820679055355,0.082299300006,0.0828392204372,0.0828135099404,0.0830963254044,0.0836362458355,0.0835591143454,0.083687666829,0.0837905088159,0.0841247452733,0.0844589817306,0.0844589817306,0.0844332712339,0.0846389552077,0.084330429247,0.0846389552077,0.0848703496782,0.0848189286847,0.0850503231552,0.085076033652,0.0852045861356,0.0851531651421,0.0849989021618,0.0853331386192,0.0852817176257,0.0852302966323,0.0854616911028,0.0854359806061,0.0855645330897,0.0856673750766,0.0856159540831,0.085898769547,0.0864129794815,0.0862330060044,0.086644373952,0.0866957949454,0.0865929529585,0.0866957949454,0.0866957949454,0.0869271894159,0.0869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m <- 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ycorr <- 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altd  <- c(1, 178, 194, 226)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('02-AP1-GSE45939-GSE45938/AG-GFP-AP1-GR-ap1-cal-Rep1-GSM1120014/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) : 1,178,194,226',bty='n')
dev.off()