Mercurial > repos > nanettec > classifier
view classifier/eqtl_genes_positions_plot.txt @ 0:ef9c2044d86a draft
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author | nanettec |
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date | Fri, 18 Mar 2016 05:15:29 -0400 |
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#setwd("/Users/nanettecoetzer/Documents/Bioinformatics/MAIZE_project/eQTL_pipeline/April_2012_pipeline_scripts/July_2012/output_July") eqtl <- read.table("all_classification.txt",sep="\t",header=TRUE) lookup <- read.table("lookup.txt",sep="\t",header=TRUE) trans_eqtl_bins <- eqtl[eqtl[,14]=="trans",15] trans_gene_bins <- eqtl[eqtl[,14]=="trans",16] cis_eqtl_bins <- eqtl[eqtl[,14]=="cis",15] cis_gene_bins <- eqtl[eqtl[,14]=="cis",16] # cis and trans in colour pdf("Rplot_eQTL_genes_positions.pdf") 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') points(cis_eqtl_bins, cis_gene_bins, type="p", pch=".", cex=2, col="blue") chr.nr = max(lookup[,2]) chr.mid = c() chr.sides = c(0) chr_labels = c() for (c in 1:chr.nr) { chr_labels <- c(chr_labels,paste("chr",c,sep="")) pos <- length(lookup[lookup[,2]==c,1])/2 end <- max(lookup[lookup[,2]==c,1]) chr.mid = c(chr.mid,pos+min(lookup[lookup[,2]==c,1])-1) chr.sides = c(chr.sides, end) } abline(v=chr.sides, lty=3, lwd=2) axis(side=1, at=chr.mid, labels= chr_labels) dev.off()