# R script for Peak Model
#  -- generated by MACS
p <- c(0.0486413714365,0.05651523943,0.0648674265072,0.0731828198087,0.0813878317833,0.081645388213,0.0814246255589,0.0814982131103,0.0816085944373,0.0816821819886,0.0809463064752,0.0811670691292,0.0809831002509,0.0805783687185,0.0807255438212,0.0807991313725,0.0806519562699,0.0806887500455,0.0802840185132,0.0800632558591,0.0809831002509,0.0811302753536,0.0809831002509,0.0810934815779,0.0806519562699,0.0807255438212,0.0805783687185,0.0804311936158,0.0805047811672,0.0803576060645,0.0803576060645,0.0801736371861,0.0800632558591,0.0802840185132,0.0806887500455,0.0803943998402,0.0803208122888,0.0804311936158,0.0806887500455,0.0805783687185,0.0802840185132,0.0803208122888,0.0804679873915,0.0800264620835,0.0794745554484,0.0794377616727,0.0792537927944,0.0792905865701,0.0789226488133,0.0788858550377,0.078628298608,0.078959442589,0.0788858550377,0.0788858550377,0.0792169990187,0.0791066176917,0.0794377616727,0.0792537927944,0.0796585243268,0.0798056994294,0.0798424932051,0.0795849367754,0.0794377616727,0.0797321118781,0.0792905865701,0.0792169990187,0.0793273803457,0.0794745554484,0.079069823916,0.0791066176917,0.0791434114674,0.0786650923837,0.078628298608,0.0781131857486,0.0782603608513,0.0782971546269,0.0779292168702,0.0779660106459,0.0781867732999,0.0778556293189,0.0783339484026,0.0787018861593,0.0789226488133,0.0794377616727,0.0795113492241,0.0796953181024,0.0798792869808,0.0799528745321,0.0798792869808,0.0802104309618,0.0799528745321,0.0797689056538,0.0795113492241,0.0796953181024,0.0798792869808,0.0801000496348,0.0805783687185,0.0805047811672,0.0806887500455,0.0808359251482,0.0809831002509,0.0811302753536,0.0812774504563,0.0810566878022,0.0810934815779,0.0810198940266,0.0808727189239,0.0807623375969,0.0805415749429,0.0803943998402,0.0805415749429,0.0805047811672,0.0804679873915,0.0806887500455,0.0806887500455,0.0807991313725,0.0806151624942,0.0806151624942,0.0807255438212,0.0806887500455,0.0807623375969,0.0809463064752,0.0812406566806,0.0807991313725,0.0809095126996,0.0807255438212,0.0806887500455,0.0806151624942,0.0807255438212,0.0807255438212,0.0803576060645,0.0803208122888,0.0800632558591,0.0800632558591,0.0794745554484,0.079069823916,0.0796217305511,0.0798424932051,0.0794009678971,0.0796953181024,0.0798424932051,0.0796585243268,0.0799896683078,0.0801736371861,0.0804311936158,0.0805415749429,0.0796585243268,0.0796585243268,0.0795481429997,0.0794745554484,0.0793273803457,0.0793641741214,0.0792169990187,0.0794377616727,0.0795481429997,0.0797689056538,0.0803943998402,0.0802840185132,0.0810198940266,0.0807623375969,0.0808727189239,0.0808359251482,0.0808359251482,0.0805415749429,0.0804311936158,0.0800264620835,0.0801000496348,0.0800632558591,0.0795849367754,0.0794009678971,0.0795113492241,0.0796953181024,0.0794009678971,0.0793641741214,0.0794009678971,0.0799160807565,0.0793641741214,0.0792537927944,0.0792905865701,0.0797689056538,0.0795849367754,0.079069823916,0.0795113492241,0.0796953181024,0.0798056994294,0.0797321118781,0.0798792869808,0.0803943998402,0.0807255438212,0.0807991313725,0.0806519562699,0.0809831002509,0.0808359251482,0.0806151624942,0.0805783687185,0.0805415749429,0.0805415749429,0.0805783687185,0.0803576060645,0.0800264620835,0.0805047811672,0.0805783687185,0.0801368434105,0.0804679873915,0.0808727189239,0.0809831002509,0.0809095126996,0.0808359251482,0.0807991313725,0.0810566878022,0.0807623375969,0.0805415749429,0.0810198940266,0.0806151624942,0.0799528745321,0.0798424932051,0.0799896683078,0.0800264620835,0.0801368434105,0.0801736371861,0.0798792869808,0.0798424932051,0.0794745554484,0.0798792869808,0.0798792869808,0.0795849367754,0.0793273803457,0.0788122674863,0.0784443297296,0.078407535954,0.0784811235053,0.0783339484026,0.0780395981973,0.0777084542162,0.0777820417676,0.0779292168702,0.078407535954,0.0782235670756,0.078959442589,0.0789226488133,0.078959442589,0.0794009678971,0.0800632558591,0.0805047811672,0.0809095126996,0.0810198940266,0.0808727189239,0.081535006886,0.0807255438212,0.0808359251482,0.0814982131103,0.0816821819886,0.0814982131103,0.081535006886,0.081535006886,0.081535006886,0.0814982131103,0.0813142442319,0.0816085944373,0.081535006886,0.0810566878022,0.0807623375969,0.0807991313725,0.0804311936158,0.0802840185132,0.0805415749429,0.0807255438212,0.0805783687185,0.0806151624942,0.0804311936158,0.0805415749429,0.0803943998402,0.0806151624942,0.0805783687185,0.0806151624942,0.0803943998402,0.0802104309618,0.0804311936158,0.0809095126996,0.0812038629049,0.0812774504563,0.0813878317833,0.0812406566806,0.0814614193346,0.0814614193346,0.081535006886,0.0817189757643,0.0818293570913,0.0813510380076,0.0813510380076,0.0811670691292,0.0817925633156,0.0818293570913,0.0820501197453,0.0823444699507,0.0824548512777,0.0827492014831,0.0828963765858,0.0829699641371,0.0831907267911,0.0835954583235,0.0834482832208,0.0834482832208,0.0831539330155,0.0826756139317,0.0822708823994,0.081866150867,0.0815718006616,0.081866150867,0.0817925633156,0.0813510380076,0.0811670691292,0.0814246255589,0.081682181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m <- 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ycorr <- 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altd  <- c(0, 38, 76, 117, 133, 139, 226, 233, 406, 447, 499, 542, 559, 593, 597)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('03-PolIV-GSE45368/PolIV-ChIP-replicate-2-GSM1103233/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) : 0,38,76,117,133,139,226,233,406,447,499,542,559,593,597',bty='n')
dev.off()