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2 #setwd("/Users/nanettecoetzer/Documents/Bioinformatics/MAIZE_project/eQTL_pipeline/April_2012_pipeline_scripts/July_2012/output_July")
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3 eqtl <- read.table("all_classification.txt",sep="\t",header=TRUE)
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4 lookup <- read.table("lookup.txt",sep="\t",header=TRUE)
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5
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6 trans_eqtl_bins <- eqtl[eqtl[,14]=="trans",15]
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7 trans_gene_bins <- eqtl[eqtl[,14]=="trans",16]
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8 cis_eqtl_bins <- eqtl[eqtl[,14]=="cis",15]
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9 cis_gene_bins <- eqtl[eqtl[,14]=="cis",16]
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10
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11 # cis and trans in colour
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12
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13 pdf("Rplot_eQTL_genes_positions.pdf")
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14 plot(trans_eqtl_bins, trans_gene_bins, type="p", pch=".", cex=2, main="", xlab="eQTL position", ylab="Gene position",col="green", xaxt='n', yaxt='n')
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15 points(cis_eqtl_bins, cis_gene_bins, type="p", pch=".", cex=2, col="blue")
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16
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17 chr.nr = max(lookup[,2])
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18 chr.mid = c()
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19 chr.sides = c(0)
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20 chr_labels = c()
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21 for (c in 1:chr.nr) {
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22 chr_labels <- c(chr_labels,paste("chr",c,sep=""))
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23 pos <- length(lookup[lookup[,2]==c,1])/2
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24 end <- max(lookup[lookup[,2]==c,1])
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25 chr.mid = c(chr.mid,pos+min(lookup[lookup[,2]==c,1])-1)
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26 chr.sides = c(chr.sides, end)
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27 }
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28 abline(v=chr.sides, lty=3, lwd=2)
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29
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30 axis(side=1, at=chr.mid, labels= chr_labels)
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31 dev.off()
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32
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