# R script for Peak Model
#  -- generated by MACS
p <- c(0.0476678074805,0.0555069464022,0.0633704304758,0.0713556403091,0.0793895404463,0.0795356113579,0.0797060274214,0.079511266206,0.0793651952944,0.0792921598386,0.0792678146867,0.0793651952944,0.0795843016618,0.079486921054,0.0795599565098,0.0795356113579,0.0794625759021,0.0795843016618,0.0797547177253,0.0798277531811,0.0796329919656,0.0795843016618,0.0793651952944,0.079511266206,0.0792434695347,0.0790487083193,0.0791947792309,0.0791704340789,0.0790730534712,0.0791704340789,0.0793895404463,0.0794138855982,0.0794138855982,0.079486921054,0.0796329919656,0.0796816822695,0.0794382307502,0.0795356113579,0.079511266206,0.0795599565098,0.0797303725733,0.0799251337888,0.0801442401562,0.0801442401562,0.080217275612,0.0803390013716,0.080558107739,0.080558107739,0.0807285238025,0.0807528689544,0.080558107739,0.0805337625871,0.0803390013716,0.0800225143965,0.0797790628772,0.0796573371175,0.0793895404463,0.0792191243828,0.0790243631673,0.0789513277116,0.0788296019519,0.0783670440652,0.0783670440652,0.0784887698249,0.0786104955845,0.0786348407365,0.0785374601287,0.0785374601287,0.0785618052807,0.0785374601287,0.0787078761922,0.0788782922558,0.0789513277116,0.078780911648,0.0785861504326,0.078440079521,0.0786835310403,0.0788052568,0.0789513277116,0.0790973986231,0.0789513277116,0.079146088927,0.079146088927,0.079511266206,0.0798034080291,0.0800225143965,0.0800955498523,0.0799738240926,0.0795356113579,0.0793165049905,0.0794382307502,0.0792191243828,0.0791217437751,0.0787565664961,0.0787565664961,0.0787078761922,0.0786104955845,0.078780911648,0.0790730534712,0.0792434695347,0.0792678146867,0.0794625759021,0.0794625759021,0.0797060274214,0.0795843016618,0.0796573371175,0.0798277531811,0.0799007886369,0.0799251337888,0.0798034080291,0.0798034080291,0.0797060274214,0.079852098333,0.0799981692446,0.0798764434849,0.0798277531811,0.0797547177253,0.0797060274214,0.0796329919656,0.079511266206,0.0795843016618,0.0798764434849,0.079852098333,0.079852098333,0.0800955498523,0.0802903110677,0.0804850722832,0.0806067980428,0.0807528689544,0.0810937010815,0.081264117145,0.0811180462334,0.081264117145,0.081239771993,0.0811910816892,0.0810693559295,0.0808502495622,0.0807041786506,0.0805337625871,0.0803876916755,0.080217275612,0.0801442401562,0.0797303725733,0.0795356113579,0.0795356113579,0.0792921598386,0.0791947792309,0.0791217437751,0.0792191243828,0.0791217437751,0.0790487083193,0.0791217437751,0.0793408501424,0.0793408501424,0.0792678146867,0.0792678146867,0.0791704340789,0.0790243631673,0.0786835310403,0.0785618052807,0.0785131149768,0.0781966280017,0.0782209731536,0.0782696634575,0.0780505570901,0.0779531764824,0.0780018667863,0.078074902242,0.0782940086094,0.078440079521,0.0782696634575,0.0785131149768,0.0784157343691,0.0783183537614,0.0785618052807,0.0785618052807,0.0785374601287,0.0785861504326,0.0786348407365,0.0786835310403,0.0788782922558,0.0787078761922,0.0787322213442,0.0786591858884,0.0784644246729,0.0787078761922,0.0787565664961,0.0786591858884,0.0787565664961,0.0786591858884,0.0786835310403,0.078780911648,0.0787322213442,0.0788296019519,0.0790973986231,0.079146088927,0.0791947792309,0.0792434695347,0.0792678146867,0.0793651952944,0.0793895404463,0.0793165049905,0.079511266206,0.0796329919656,0.0795843016618,0.0797060274214,0.079852098333,0.0798764434849,0.0797547177253,0.0797060274214,0.0796573371175,0.0797547177253,0.0796086468137,0.0794382307502,0.079511266206,0.079486921054,0.0795599565098,0.0798764434849,0.0800225143965,0.08019293046,0.0803146562197,0.0804607271313,0.0806067980428,0.0807285238025,0.0806798334986,0.0805824528909,0.080558107739,0.0803633465235,0.080558107739,0.0806067980428,0.0805824528909,0.0808502495622,0.0809232850179,0.0810693559295,0.0811667365373,0.0811180462334,0.0809232850179,0.080898939866,0.0807772141064,0.0807528689544,0.0809476301699,0.0808259044102,0.0808015592583,0.0809719753218,0.0810206656257,0.0811423913853,0.0811910816892,0.0813858429046,0.0810937010815,0.0809232850179,0.0808015592583,0.0806798334986,0.0806067980428,0.080217275612,0.0800955498523,0.0801198950042,0.08019293046,0.0800712047004,0.0803146562197,0.0804120368274,0.0803146562197,0.08019293046,0.0801442401562,0.08019293046,0.0803876916755,0.0803146562197,0.0803876916755,0.0803146562197,0.0801685853081,0.08019293046,0.0800955498523,0.0800712047004,0.0802903110677,0.0803876916755,0.080217275612,0.080217275612,0.0801198950042,0.0803390013716,0.0804850722832,0.0806554883467,0.0810450107776,0.0812884622969,0.081239771993,0.0813614977527,0.0816292944239,0.0817753653355,0.0820431620068,0.0820918523106,0.0823353038299,0.0824083392857,0.082310958678,0.0824083392857,0.0825787553492,0.0827248262608,0.0825544101973,0.082651790805,0.0826031005012,0.0827248262608,0.082651790805,0.0826274456531,0.0827004811089,0.0827491714128,0.082651790805,0.0826274456531,0.0829195874763,0.0829195874763,0.0831143486917,0.0832117292994,0.0834308356668,0.0836499420342,0.0839177387054,0.0840881547689,0.0843559514402,0.0845507126556,0.0846724384153,0.08489154478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m <- 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ycorr <- 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altd  <- c(1, 34, 542, 583)
x <- seq.int((length(p)-1)/2*-1,(length(p)-1)/2)
pdf('39-PhyA-GSE48770/PhyA-GFP_1-GSM1184360/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) : 1,34,542,583',bty='n')
dev.off()