# R script for Peak Model
#  -- generated by MACS
p <- c(0.0494629226494,0.0575869655356,0.0654610378715,0.0739287902644,0.0816778773251,0.0816466310063,0.0814903994123,0.0808029803989,0.0806779951237,0.0798030981975,0.0795843739659,0.079428142372,0.0793656497344,0.0791781718216,0.0792406644592,0.0791781718216,0.0795843739659,0.0798343445163,0.0798343445163,0.0806467488049,0.0809592119928,0.0807717340801,0.0810529509492,0.0806779951237,0.080334285617,0.0800530687478,0.0793656497344,0.0792406644592,0.0793031570968,0.0792094181404,0.079115679184,0.0793968960532,0.079271910778,0.0790844328653,0.0798030981975,0.0798655908351,0.0798655908351,0.0798968371539,0.079428142372,0.0792094181404,0.0788344623149,0.0786469844022,0.0788032159961,0.0788657086337,0.0786782307209,0.0790531865465,0.0792406644592,0.0793344034156,0.0798968371539,0.0800530687478,0.0803655319358,0.0802717929794,0.0801155613854,0.0803967782546,0.080178054023,0.0797718518787,0.0801468077042,0.080021822429,0.0795531276471,0.0793344034156,0.0790219402277,0.0790531865465,0.0789594475901,0.0789594475901,0.0790844328653,0.0793656497344,0.0790844328653,0.0791469255028,0.0792094181404,0.0790531865465,0.0797093592411,0.0796468666035,0.079428142372,0.0789594475901,0.0788969549525,0.0789594475901,0.079271910778,0.0798343445163,0.0798343445163,0.0796468666035,0.0790844328653,0.0793656497344,0.0797406055599,0.0799905761103,0.0798968371539,0.079428142372,0.0795218813284,0.079271910778,0.079271910778,0.0791781718216,0.0795531276471,0.0795218813284,0.0798655908351,0.0799280834727,0.080021822429,0.0805842561673,0.0805530098485,0.0808967193553,0.081084197268,0.0809592119928,0.0803655319358,0.0802093003418,0.0794906350096,0.0797406055599,0.0796156202847,0.0791469255028,0.0785844917646,0.0780845506639,0.0781157969827,0.0784595064894,0.0788344623149,0.0790844328653,0.0793968960532,0.0794906350096,0.0799280834727,0.0802093003418,0.0802093003418,0.0800843150666,0.0795218813284,0.0796468666035,0.0795843739659,0.079271910778,0.0793656497344,0.079115679184,0.0786157380834,0.0785844917646,0.0786782307209,0.078521999127,0.0788032159961,0.078521999127,0.0784282601706,0.0784282601706,0.0782407822578,0.0781470433015,0.0784282601706,0.0788344623149,0.0789594475901,0.0794593886908,0.0796781129223,0.0795218813284,0.0798030981975,0.0802405466606,0.0802093003418,0.0802717929794,0.0802405466606,0.0798655908351,0.0798343445163,0.0798030981975,0.0798343445163,0.0805530098485,0.0808342267177,0.0805530098485,0.0805217635297,0.0808029803989,0.0806779951237,0.0808654730365,0.0806467488049,0.0804905172109,0.0803655319358,0.0802093003418,0.0798655908351,0.080021822429,0.0803030392982,0.0801468077042,0.0805842561673,0.0803967782546,0.0806779951237,0.0804280245734,0.0803967782546,0.0803967782546,0.0801155613854,0.080334285617,0.0806467488049,0.0804592708921,0.080021822429,0.0794906350096,0.0793031570968,0.0793344034156,0.0793031570968,0.0788344623149,0.0786782307209,0.078209535939,0.0777720874759,0.0778658264323,0.0781782896203,0.0788032159961,0.0787719696773,0.0792406644592,0.0795843739659,0.0798968371539,0.0804280245734,0.0806779951237,0.0802717929794,0.080178054023,0.0795531276471,0.0793344034156,0.079428142372,0.0791781718216,0.0788344623149,0.0784595064894,0.0783032748954,0.0783345212142,0.0784282601706,0.0784907528082,0.0787094770397,0.0786157380834,0.0787094770397,0.0781470433015,0.0781470433015,0.0786469844022,0.0783345212142,0.0775846095632,0.0775846095632,0.077615855882,0.0777095948384,0.077459624288,0.0771159147813,0.0776471022008,0.0774283779692,0.0772096537377,0.0773971316504,0.0776783485196,0.0779908117075,0.0778033337947,0.0781470433015,0.0780220580263,0.0779595653887,0.0778658264323,0.0776783485196,0.0777095948384,0.0778658264323,0.0779908117075,0.0778970727511,0.0783032748954,0.0781157969827,0.0779908117075,0.0785844917646,0.0789906939089,0.0793031570968,0.079115679184,0.0791781718216,0.0793656497344,0.0794906350096,0.079428142372,0.0795531276471,0.0802405466606,0.0801155613854,0.0796781129223,0.0798968371539,0.080178054023,0.0799593297915,0.0802405466606,0.080334285617,0.0803030392982,0.0798655908351,0.0799280834727,0.0799905761103,0.0799593297915,0.0800530687478,0.080021822429,0.080021822429,0.0794906350096,0.0795531276471,0.0795218813284,0.080021822429,0.0799905761103,0.080021822429,0.080334285617,0.0806155024861,0.0805842561673,0.0807717340801,0.080927965674,0.0806155024861,0.0807717340801,0.0805530098485,0.080178054023,0.0797718518787,0.0798968371539,0.0797093592411,0.0798655908351,0.0799280834727,0.0804592708921,0.0806779951237,0.0806779951237,0.081084197268,0.0817091236439,0.0818028626002,0.0817091236439,0.0816153846875,0.0813341678184,0.0811779362244,0.0805530098485,0.0805842561673,0.0807092414425,0.0807404877613,0.0804905172109,0.0811466899056,0.0812716751808,0.081240428862,0.0816778773251,0.0819278478754,0.0823652963385,0.0820215868318,0.081834108919,0.0814591530935,0.0814279067747,0.0810529509492,0.0816466310063,0.0818966015566,0.082146572107,0.0817091236439,0.081834108919,0.0825527742513,0.0828339911204,0.0832401932647,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m <- 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ycorr <- 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altd  <- c(0, 44, 72, 94, 97, 108, 132, 426, 468, 499, 525, 559, 585)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('48-PIF1-PIF4-GSE43286/PIF4-peaks-3-GSM1059965/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) : 0,44,72,94,97,108,132,426,468,499,525,559,585',bty='n')
dev.off()