Mercurial > repos > nanettec > classifier
comparison 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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-1:000000000000 | 0:ef9c2044d86a |
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1 | |
2 #setwd("/Users/nanettecoetzer/Documents/Bioinformatics/MAIZE_project/eQTL_pipeline/April_2012_pipeline_scripts/July_2012/output_July") | |
3 eqtl <- read.table("all_classification.txt",sep="\t",header=TRUE) | |
4 lookup <- read.table("lookup.txt",sep="\t",header=TRUE) | |
5 | |
6 trans_eqtl_bins <- eqtl[eqtl[,14]=="trans",15] | |
7 trans_gene_bins <- eqtl[eqtl[,14]=="trans",16] | |
8 cis_eqtl_bins <- eqtl[eqtl[,14]=="cis",15] | |
9 cis_gene_bins <- eqtl[eqtl[,14]=="cis",16] | |
10 | |
11 # cis and trans in colour | |
12 | |
13 pdf("Rplot_eQTL_genes_positions.pdf") | |
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') | |
15 points(cis_eqtl_bins, cis_gene_bins, type="p", pch=".", cex=2, col="blue") | |
16 | |
17 chr.nr = max(lookup[,2]) | |
18 chr.mid = c() | |
19 chr.sides = c(0) | |
20 chr_labels = c() | |
21 for (c in 1:chr.nr) { | |
22 chr_labels <- c(chr_labels,paste("chr",c,sep="")) | |
23 pos <- length(lookup[lookup[,2]==c,1])/2 | |
24 end <- max(lookup[lookup[,2]==c,1]) | |
25 chr.mid = c(chr.mid,pos+min(lookup[lookup[,2]==c,1])-1) | |
26 chr.sides = c(chr.sides, end) | |
27 } | |
28 abline(v=chr.sides, lty=3, lwd=2) | |
29 | |
30 axis(side=1, at=chr.mid, labels= chr_labels) | |
31 dev.off() | |
32 |