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qqman4Manhattanplots.R
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qqman4Manhattanplots.R
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library('qqman')
library('tidyverse')
library(calibrate)
Gap.dat <- read.csv("GAPIT.MLM.Color.qqBOI.csv", head=T)
For.Gap.dat <- Gap.dat
-log10(For.Gap.dat$P[1])
Chr03 <- which(For.Gap.dat$CHR == 3)
Chr03 <- For.Gap.dat[Chr03,]
Ordf <- Chr03[which(Chr03$BP > 5000000 & Chr03$BP < 5200000),]
Chr05 <- which(For.Gap.dat$CHR == 5)
Chr05 <- For.Gap.dat[Chr05,]
Ydf <- Chr05[which(Chr05$BP > 29935615 & Chr05$BP < 30065947),]
Chr07 <- which(For.Gap.dat$CHR == 7)
Chr07 <- For.Gap.dat[Chr07,]
Y2df <- Chr07[which(Chr07$BP > 38656562 & Chr07$BP < 39560030),]
OrSNPs <- as.character(Ordf$SNP)
YSNPs <- as.character(Ydf$SNP)
Y2SNPs <- as.character(Y2df$SNP)
SNPsofFun <- c(OrSNPs, YSNPs, Y2SNPs)
fix(manhattan)
# set textxy
pdf(file="RG.Taproot.pdf", bg="white", width=10, height=6)
manhattan(For.Gap.dat, main="Taproot Color", ylim=c(0,20),cex.lab=1.25, cex.axis = 1.25, cex.main=1.5,
col=c("#C5050C","grey"), suggestiveline=F, genomewideline=7.86, chrlabs=c("1","2","3","4","5","6","7","8","9"),
annotatePval = 0.000000007, highlight = SNPsofFun)
dev.off()
pdf(file="OB.Taproot.pdf", bg="white", width=10, height=6)
manhattan(For.Gap.dat, main="Taproot Color", ylim=c(0,20),cex.lab=1.25, cex.axis = 1.25, cex.main=1.5,
col=c("Orange","Blue"), suggestiveline=F, genomewideline=7.86, chrlabs=c("1","2","3","4","5","6","7","8","9"),
annotatePval = 0.000000007, highlight = SNPsofFun)
dev.off()
Gap.dat <- read.csv("GAPIT.MLM.Carotene.qqBOI.csv", head=T)
For.Gap.dat <- Gap.dat
-log10(For.Gap.dat$P[1])
Chr03 <- which(For.Gap.dat$CHR == 3)
Chr03 <- For.Gap.dat[Chr03,]
Ordf <- Chr03[which(Chr03$BP > 5000000 & Chr03$BP < 5200000),]
Chr05 <- which(For.Gap.dat$CHR == 5)
Chr05 <- For.Gap.dat[Chr05,]
Ydf <- Chr05[which(Chr05$BP > 29935615 & Chr05$BP < 30065947),]
Chr07 <- which(For.Gap.dat$CHR == 7)
Chr07 <- For.Gap.dat[Chr07,]
Y2df <- Chr07[which(Chr07$BP > 38656562 & Chr07$BP < 39560030),]
OrSNPs <- as.character(Ordf$SNP)
YSNPs <- as.character(Ydf$SNP)
Y2SNPs <- as.character(Y2df$SNP)
SNPsofFun <- c(OrSNPs, YSNPs, Y2SNPs)
pdf(file="RG.alpabeta.pdf", bg="white", width=10, height=6)
manhattan(For.Gap.dat, main="Percent ?? + ?? carotene", ylim=c(0,15),cex.lab=1.25, cex.axis = 1.25, cex.main=1.5,
col=c("#C5050C","grey"), suggestiveline=F, genomewideline=7.86, chrlabs=c("1","2","3","4","5","6","7","8","9"),
annotatePval = 0.000000007, highlight = SNPsofFun)
dev.off()
pdf(file="OB.alpabeta.pdf", bg="white", width=10, height=6)
manhattan(For.Gap.dat, main="Percent ?? + ?? carotene", ylim=c(0,15),cex.lab=1.25, cex.axis = 1.25, cex.main=1.5,
col=c("Orange","Blue"), suggestiveline=F, genomewideline=7.86, chrlabs=c("1","2","3","4","5","6","7","8","9"),
annotatePval = 0.000000007, highlight = SNPsofFun)
dev.off()
Gap.dat <- read.csv("GAPIT.MLM.Lutein.qqBOI.csv", head=T)
For.Gap.dat <- Gap.dat
-log10(For.Gap.dat$P[1])
Chr03 <- which(For.Gap.dat$CHR == 3)
Chr03 <- For.Gap.dat[Chr03,]
Ordf <- Chr03[which(Chr03$BP > 5000000 & Chr03$BP < 5200000),]
Chr05 <- which(For.Gap.dat$CHR == 5)
Chr05 <- For.Gap.dat[Chr05,]
Ydf <- Chr05[which(Chr05$BP > 29935615 & Chr05$BP < 30065947),]
Chr07 <- which(For.Gap.dat$CHR == 7)
Chr07 <- For.Gap.dat[Chr07,]
Y2df <- Chr07[which(Chr07$BP > 38656562 & Chr07$BP < 39560030),]
OrSNPs <- as.character(Ordf$SNP)
YSNPs <- as.character(Ydf$SNP)
Y2SNPs <- as.character(Y2df$SNP)
SNPsofFun <- c(OrSNPs, YSNPs, Y2SNPs)
pdf(file="RG.Lutein.Gap.pdf", bg="white", width=10, height=6)
manhattan(For.Gap.dat,main=" Percent Lutein", ylim=c(0,15),cex.lab=1.25, cex.axis = 1.25, cex.main=1.5,col=c("#C5050C","grey"), suggestiveline=F, genomewideline=7.86, chrlabs=c("1","2","3","4","5","6","7","8","9"),
annotatePval = 0.000000007, highlight = SNPsofFun)
dev.off()
pdf(file="OB.Lutein.pdf", bg="white", width=10, height=6)
manhattan(For.Gap.dat, main="Percent Lutein", ylim=c(0,15),cex.lab=1.25, cex.axis = 1.25, cex.main=1.5,
col=c("Orange","Blue"), suggestiveline=F, genomewideline=7.86, chrlabs=c("1","2","3","4","5","6","7","8","9"),
annotatePval = 0.000000007, highlight = SNPsofFun)
dev.off()