# R script for Peak Model
#  -- generated by MACS
p <- c(0.0432958710912,0.0501981114101,0.0580130446638,0.065770934609,0.0731865647037,0.0744985607973,0.0745556041057,0.07512603719,0.0755253403489,0.07512603719,0.0742133442552,0.0751830804984,0.0739281277131,0.0731295213952,0.0730724780868,0.0725020450026,0.0722738717689,0.0714182221426,0.0705055292079,0.0705625725163,0.0703343992826,0.0695928362732,0.0695928362732,0.0704484858995,0.0695357929647,0.0689653598805,0.0692505764226,0.0692505764226,0.0694217063479,0.0687371866468,0.0687942299553,0.0687942299553,0.0687371866468,0.0678815370205,0.0687371866468,0.0689653598805,0.0685660567216,0.06862310003,0.0685660567216,0.0688512732637,0.0691935331142,0.0691935331142,0.0698780528153,0.0686801433384,0.0682237968711,0.0683949267963,0.0693646630395,0.0694787496563,0.0698210095068,0.0706766591331,0.0698780528153,0.0696498795816,0.0701062260489,0.0718175253016,0.072559088311,0.0715323087595,0.0718175253016,0.0722738717689,0.0717604819931,0.070391442591,0.0717034386847,0.0721027418437,0.0722738717689,0.0723879583858,0.07187456861,0.0726731749279,0.0716463953763,0.0708477890584,0.0719886552268,0.0733006513205,0.0726731749279,0.072559088311,0.0715893520679,0.0715893520679,0.0730724780868,0.0730154347784,0.0732436080121,0.0731865647037,0.0731295213952,0.0724450016942,0.0719886552268,0.0721027418437,0.0726161316194,0.0732436080121,0.0712470922174,0.0713611788342,0.0708477890584,0.0710759622921,0.0696498795816,0.0695357929647,0.0696498795816,0.0694217063479,0.0692505764226,0.0684519701047,0.0695928362732,0.0698780528153,0.0703343992826,0.0709618756753,0.0717604819931,0.0723879583858,0.0723309150773,0.0714182221426,0.0716463953763,0.0711900489089,0.0705055292079,0.0698210095068,0.0699921394321,0.0687371866468,0.0683949267963,0.0679956236374,0.0687942299553,0.0691935331142,0.0692505764226,0.0685090134132,0.0686801433384,0.0691935331142,0.0686801433384,0.0690224031889,0.0685660567216,0.067938580329,0.0682237968711,0.0689083165721,0.0691364898058,0.0710189189837,0.0713041355258,0.0717604819931,0.0721027418437,0.0719886552268,0.0731865647037,0.0735288245542,0.0726731749279,0.072559088311,0.0728443048531,0.0721597851521,0.0710189189837,0.0700491827405,0.0703343992826,0.0717034386847,0.0722168284605,0.0730724780868,0.0735288245542,0.0739851710215,0.073642911171,0.0732436080121,0.0732436080121,0.0738710844047,0.0731295213952,0.0727872615447,0.0716463953763,0.0709048323668,0.0702203126658,0.0694217063479,0.0693076197311,0.0695357929647,0.0699350961237,0.0694787496563,0.0687942299553,0.0681097102542,0.0677674504037,0.0674251905532,0.0683949267963,0.0689083165721,0.0685660567216,0.0684519701047,0.0693646630395,0.0701062260489,0.07079074575,0.0712470922174,0.0717034386847,0.0726731749279,0.07187456861,0.0727302182363,0.073642911171,0.0743274308721,0.07404221433,0.0741563009468,0.0750689938815,0.0756964702742,0.0751830804984,0.0742703875636,0.0736999544794,0.0723879583858,0.0713041355258,0.0708477890584,0.0700491827405,0.0692505764226,0.0687942299553,0.0681097102542,0.0691935331142,0.0693076197311,0.070391442591,0.0706196158247,0.0707337024416,0.0700491827405,0.070391442591,0.0701062260489,0.0699350961237,0.0705625725163,0.0703343992826,0.0709618756753,0.0716463953763,0.0719316119184,0.0715893520679,0.0717034386847,0.0720456985352,0.0723309150773,0.0728443048531,0.0722168284605,0.0721597851521,0.0717034386847,0.0713041355258,0.070391442591,0.0703343992826,0.0701062260489,0.0699921394321,0.0702203126658,0.0693646630395,0.0696498795816,0.0690224031889,0.0687371866468,0.0677674504037,0.0678815370205,0.0681667535626,0.0685090134132,0.0679956236374,0.0680526669458,0.0693076197311,0.0691935331142,0.0698780528153,0.0706196158247,0.0716463953763,0.0722168284605,0.0719886552268,0.0715893520679,0.0724450016942,0.0719886552268,0.0709618756753,0.0713041355258,0.0707337024416,0.0702773559742,0.0699921394321,0.0698210095068,0.0706766591331,0.0712470922174,0.0717604819931,0.0729013481616,0.0735858678626,0.0739281277131,0.0745556041057,0.0745556041057,0.0743274308721,0.0742703875636,0.0750689938815,0.0756964702742,0.0750119505731,0.0749549072647,0.0749549072647,0.0751830804984,0.0750689938815,0.0756964702742,0.0761528167415,0.0764380332836,0.0753542104236,0.0748978639563,0.0753542104236,0.0750119505731,0.0748408206479,0.0737569977879,0.0743274308721,0.0751830804984,0.0752401238068,0.0753542104236,0.0755253403489,0.0752401238068,0.074726734031,0.0750689938815,0.0745556041057,0.0757535135826,0.0756964702742,0.0751830804984,0.0747837773394,0.0743844741805,0.0742133442552,0.0743844741805,0.0751830804984,0.0750119505731,0.0760387301247,0.0757535135826,0.0760957734331,0.0763239466668,0.0776359427605,0.0772936829099,0.0776359427605,0.0788338522373,0.0787197656205,0.0792331553962,0.0795754152468,0.0803169782562,0.0803169782562,0.0806592381068,0.0800888050225,0.081229671191,0.0819712342004,0.0821994074341,0.0822564507425,0.0815148877331,0.0814008011162,0.0814578444246,0.0814578444246,0.0810585412657,0.0818571475836,0.0827127972099,0.0829409704436,0.0821994074341,0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m <- 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ycorr <- 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altd  <- c(127, 559)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('82-FUL-GSE108455/FUL-pistil-rep2-GSM2898772/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) : 127,559',bty='n')
dev.off()