# R script for Peak Model
#  -- generated by MACS
p <- c(0.0481301482553,0.0561217394759,0.064339081861,0.0723758233145,0.0803222643022,0.0807286163982,0.0805028652338,0.0805480154667,0.080818916864,0.0809543675626,0.0811349684942,0.0814510201244,0.0814961703572,0.0816316210559,0.0820379731519,0.0821734238505,0.0825797759465,0.0824443252478,0.0825797759465,0.082760376878,0.0828055271109,0.0825797759465,0.0824443252478,0.0823088745492,0.0820831233848,0.0818573722203,0.081586470823,0.0817219215217,0.0814961703572,0.0814510201244,0.0814510201244,0.0816316210559,0.0816316210559,0.0817670717546,0.081992822919,0.081992822919,0.0820831233848,0.0821282736176,0.0821734238505,0.0822637243163,0.0821282736176,0.081992822919,0.0820831233848,0.0823088745492,0.0821734238505,0.0824443252478,0.0824894754807,0.0824443252478,0.0824443252478,0.0823991750149,0.0826249261794,0.0825797759465,0.0823540247821,0.0820831233848,0.0818122219874,0.081586470823,0.0814961703572,0.0812704191928,0.0812704191928,0.0811349684942,0.0808640670969,0.0808640670969,0.0806834661653,0.0806383159324,0.0809995177955,0.0806834661653,0.0805480154667,0.0805480154667,0.0804577150009,0.0803222643022,0.0803222643022,0.0800513629049,0.0800965131378,0.080006212672,0.0795998605761,0.0797804615076,0.0796901610419,0.0795547103432,0.0793741094117,0.0794644098774,0.0794644098774,0.0796901610419,0.0799159122063,0.0799610624392,0.080006212672,0.0800513629049,0.0803674145351,0.0804577150009,0.0807737666311,0.0805480154667,0.0807286163982,0.0806834661653,0.0807286163982,0.0809543675626,0.0811349684942,0.0809995177955,0.080818916864,0.0809995177955,0.080818916864,0.0808640670969,0.080818916864,0.0809995177955,0.0809543675626,0.0808640670969,0.0809092173297,0.0810446680284,0.0811349684942,0.0811801187271,0.0813155694257,0.0816767712888,0.0817670717546,0.0821282736176,0.0823540247821,0.0823540247821,0.0823540247821,0.0824894754807,0.0825346257136,0.0824894754807,0.0823088745492,0.0821282736176,0.0819476726861,0.0815413205901,0.0814058698915,0.0815413205901,0.0814961703572,0.0814058698915,0.0814058698915,0.0813155694257,0.0813607196586,0.0812252689599,0.0814058698915,0.0814961703572,0.0813155694257,0.0808640670969,0.0809092173297,0.0809543675626,0.0806834661653,0.0807737666311,0.080818916864,0.0810446680284,0.0809092173297,0.080818916864,0.0810446680284,0.0813607196586,0.0814058698915,0.0814058698915,0.0814961703572,0.0814961703572,0.0814961703572,0.0814058698915,0.0814961703572,0.0817219215217,0.0814961703572,0.0813607196586,0.0811801187271,0.0811349684942,0.0812252689599,0.0812704191928,0.0813607196586,0.0812704191928,0.0810898182613,0.080818916864,0.0808640670969,0.0806834661653,0.0805931656995,0.0803222643022,0.080006212672,0.0798256117405,0.0798256117405,0.0797804615076,0.0797353112747,0.079645010809,0.0795547103432,0.0795547103432,0.0795998605761,0.0796901610419,0.0797804615076,0.0798256117405,0.0795998605761,0.0796901610419,0.0795547103432,0.0795095601103,0.0793741094117,0.0794644098774,0.0792838089459,0.079238658713,0.0794644098774,0.0793741094117,0.0793741094117,0.0794192596445,0.079645010809,0.0798707619734,0.0801416633707,0.0801868136036,0.080412564768,0.0806834661653,0.0804577150009,0.0804577150009,0.0809092173297,0.0809995177955,0.0810446680284,0.080818916864,0.0810446680284,0.0810898182613,0.0810898182613,0.0811349684942,0.0813155694257,0.0814510201244,0.0812704191928,0.0811801187271,0.0813607196586,0.081586470823,0.0814058698915,0.0813155694257,0.0813155694257,0.0812704191928,0.0811801187271,0.0810898182613,0.0811801187271,0.0814058698915,0.0811801187271,0.0814510201244,0.0814058698915,0.0816316210559,0.0817670717546,0.0817670717546,0.0816767712888,0.0818573722203,0.081586470823,0.0813155694257,0.0811349684942,0.0807737666311,0.0807286163982,0.0805480154667,0.0804577150009,0.0802771140694,0.0802771140694,0.0801868136036,0.0804577150009,0.0802771140694,0.0804577150009,0.0803674145351,0.080412564768,0.0806834661653,0.0808640670969,0.0810898182613,0.0813607196586,0.0814510201244,0.0813155694257,0.0816316210559,0.0818122219874,0.0821734238505,0.0823540247821,0.0824894754807,0.0824443252478,0.0824894754807,0.0825797759465,0.0824443252478,0.0823991750149,0.0823540247821,0.0822185740834,0.0820831233848,0.0820831233848,0.0818122219874,0.0818122219874,0.0816767712888,0.0815413205901,0.0815413205901,0.0814058698915,0.0811801187271,0.0811801187271,0.0809995177955,0.0809092173297,0.0809092173297,0.0809543675626,0.0808640670969,0.0809995177955,0.0812252689599,0.081586470823,0.0818122219874,0.0822185740834,0.0827152266451,0.0828506773438,0.0832118792069,0.0833021796726,0.0837536820015,0.0838439824673,0.0839794331659,0.0840697336317,0.0841148838646,0.083934282933,0.0838439824673,0.0842051843303,0.0840697336317,0.0840697336317,0.0840697336317,0.0840245833988,0.0841148838646,0.0840697336317,0.0843857852619,0.0845212359605,0.0843857852619,0.0840245833988,0.0841148838646,0.0841600340975,0.0842051843303,0.0842954847961,0.0841600340975,0.0842051843303,0.0841148838646,0.0838891327001,0.0840697336317,0.084340635029,0.0841600340975,0.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m <- 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ycorr <- 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altd  <- c(0, 37, 94, 118, 135, 210, 306, 371, 382, 405, 474, 482, 519, 555, 564)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('98-HDP-GSE89318/HDP2-IP-rep1-GSM2365922/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) : 0,37,94,118,135,210,306,371,382,405,474,482,519,555,564',bty='n')
dev.off()