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190301_plot_chromosomes.R
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190301_plot_chromosomes.R
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#!/usr/bin/env Rscript
args = commandArgs(trailingOnly=TRUE)
# args[1] = scripts directory
# args[2] = working directory
# args[3] = condition1
# args[4] = condition2
library("Hmisc")
genome <- function (scriptdir, inputdir, inputfile, output){
##genome-wide "screen" plot for fitted slope
allgenes <- data.frame(genes = read.csv(paste(scriptdir,'/gene_locations_names_2',sep = ''), sep="\t", header = FALSE)[,1], number=read.csv(paste(scriptdir,'/gene_locations_names_2',sep = ''), sep="\t", header = FALSE)[,2])
slopes <- data.frame(genes = read.csv(paste(inputdir, inputfile, sep=""), sep=",")[,1], avg = read.csv(paste(inputdir, inputfile, sep=""), sep=",")[,2], std = read.csv(paste(inputdir, inputfile, sep=""), sep=",")[,3])
allslopes <- merge(allgenes, slopes, all.y=TRUE)
allslopes <- allslopes[order(allslopes$number), ]
pdf(paste(inputdir, output, ".pdf", sep=""), width=11, height=8.5)
par(mfrow=c(4,1), mar=c(3,5,3,2))
print(head(allslopes))
#chromosome1
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr1', sep = ': '))
segments(0,0,230218,0)
chr1x <- vector()
chr1y <- vector()
for(i in 1:length(allslopes$genes)){
chr = substring(allslopes[i,1],2,2)
if(chr == 'A'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(151465), y = c(0), pch = 15, col = 'red')
chr1x <- append(chr1x, allslopes[i,2])
chr1y <- append(chr1y, allslopes[i,3])
# }
# }
}
}
#lines(chr1x, chr1y, col = 'blue')
#chromosome2
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr2', sep = ': '))
segments(0,0,813184,0)
chr2x <- vector()
chr2y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'B'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(238207), y = c(0), pch = 15, col = 'red')
chr2x <- append(chr2x, allslopes[i,2])
chr2y <- append(chr2y, allslopes[i,3])
# }
# }
}
}
# segments(238207,0,513184,0, col = 'orange', lwd = 3)
points(x = c(238207), y = c(0), pch = 15, col = 'red')
# lines(chr2x, chr2y, col = 'blue')
#chromosome3
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr3', sep = ': '))
segments(0,0,316620,0)
chr3x <- vector()
chr3y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'C'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(114385), y = c(0), pch = 15, col = 'red')
chr3x <- append(chr3x, allslopes[i,2])
chr3y <- append(chr3y, allslopes[i,3])
# }
# }
}
}
# lines(chr3x, chr3y, col = 'blue')
#chromosome4
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr4', sep = ': '))
segments(0,0,1531933,0)
chr4x <- vector()
chr4y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'D'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
chr4x <- append(chr4x, allslopes[i,2])
chr4y <- append(chr4y, allslopes[i,3])
# }
# }
}
}
# lines(chr4x, chr4y, col = 'blue')
# segments(300000,0,1231933,0, col = 'orange', lwd = 3)
# segments(1154216,0,1161320,0, col = 'orange', lwd = 5)
points(x = c(449711), y = c(0), pch = 15, col = 'red')
# segments(1443403,0,1441433,0,col = 'red', lwd = 5)
#chromosome5
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr5', sep = ': '))
segments(0,0,576874,0)
chr5x <- vector()
chr5y <- vector()
for(i in 1:length(allslopes$genes)){
chr = substring(allslopes[i,1],2,2)
if(chr == 'E'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(151987), y = c(0), pch = 15, col = 'red')
chr5x <- append(chr5x, allslopes[i,2])
chr5y <- append(chr5y, allslopes[i,3])
# }
# }
}
}
# lines(chr5x, chr5y, col = 'blue')
#chromosome6
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr6', sep = ': '))
segments(0,0,270161,0)
chr6x <- vector()
chr6y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'F'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(148510), y = c(0), pch = 15, col = 'red')
chr6x <- append(chr6x, allslopes[i,2])
chr6y <- append(chr6y, allslopes[i,3])
# }
# }
}
}
# lines(chr6x, chr6y, col = 'blue')
#chromosome7
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr7', sep = ': '))
segments(0,0,1090940,0)
chr7x <- vector()
chr7y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'G'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(497038), y = c(0), pch = 15, col = 'red')
chr7x <- append(chr7x, allslopes[i,2])
chr7y <- append(chr7y, allslopes[i,3])
# }
# }
}
}
# lines(chr7x, chr7y, col = 'blue')
#chromosome8
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr8', sep = ': '))
segments(0,0,562643,0)
chr8x <- vector()
chr8y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'H'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
chr8x <- append(chr8x, allslopes[i,2])
chr8y <- append(chr8y, allslopes[i,3])
# }
# }
}
}
# lines(chr8x, chr8y, col = 'blue')
# segments(300000,0,1231933,0, col = 'orange', lwd = 3)
# segments(1154216,0,1161320,0, col = 'orange', lwd = 5)
points(x = c(105703), y = c(0), pch = 15, col = 'red')
# segments(1443403,0,1441433,0,col = 'red', lwd = 5)
#chromosome9
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr9', sep = ': '))
segments(0,0,439888,0)
chr9x <- vector()
chr9y <- vector()
for(i in 1:length(allslopes$genes)){
chr = substring(allslopes[i,1],2,2)
if(chr == 'I'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(355629), y = c(0), pch = 15, col = 'red')
chr9x <- append(chr9x, allslopes[i,2])
chr9y <- append(chr9y, allslopes[i,3])
# }
# }
}
}
# lines(chr9x, chr9y, col = 'blue')
#chromosome10
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr10', sep = ': '))
segments(0,0,745751,0)
chr10x <- vector()
chr10y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'J'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(436425), y = c(0), pch = 15, col = 'red')
chr10x <- append(chr10x, allslopes[i,2])
chr10y <- append(chr10y, allslopes[i,3])
# }
# }
}
}
# lines(chr10x, chr10y, col = 'blue')
#chromosome11
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr11', sep = ': '))
segments(0,0,666816,0)
chr11x <- vector()
chr11y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'K'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(440246), y = c(0), pch = 15, col = 'red')
chr11x <- append(chr11x, allslopes[i,2])
chr11y <- append(chr11y, allslopes[i,3])
# }
# }
}
}
# lines(chr11x, chr11y, col = 'blue')
# segments(294610,0,296193,0,col = 'orange', lwd = 5)
#chromosome12
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr12', sep = ': '))
segments(0,0,1078177,0)
chr12x <- vector()
chr12y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'L'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
chr12x <- append(chr12x, allslopes[i,2])
chr12y <- append(chr12y, allslopes[i,3])
# }
# }
}
}
# lines(chr12x, chr12y, col = 'blue')
# segments(300000,0,1231933,0, col = 'orange', lwd = 3)
# segments(1154216,0,1161320,0, col = 'orange', lwd = 5)
points(x = c(150947), y = c(0), pch = 15, col = 'red')
# segments(1443403,0,1441433,0,col = 'red', lwd = 5)
#chromosome13
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr13', sep = ': '))
segments(0,0,924431,0)
chr13x <- vector()
chr13y <- vector()
for(i in 1:length(allslopes$genes)){
chr = substring(allslopes[i,1],2,2)
if(chr == 'M'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(268031), y = c(0), pch = 15, col = 'red')
chr13x <- append(chr13x, allslopes[i,2])
chr13y <- append(chr13y, allslopes[i,3])
# }
# }
}
}
# lines(chr13x, chr13y, col = 'blue')
#chromosome14
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr14', sep = ': '))
segments(0,0,784333,0)
chr14x <- vector()
chr14y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'N'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(628758), y = c(0), pch = 15, col = 'red')
chr14x <- append(chr14x, allslopes[i,2])
chr14y <- append(chr14y, allslopes[i,3])
# }
# }
}
}
# lines(chr14x, chr14y, col = 'blue')
#chromosome15
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr15', sep = ': '))
segments(0,0,1091291,0)
chr15x <- vector()
chr15y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'O'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
points(x = c(326702), y = c(0), pch = 15, col = 'red')
chr15x <- append(chr15x, allslopes[i,2])
chr15y <- append(chr15y, allslopes[i,3])
# }
# }
}
}
# lines(chr15x, chr15y, col = 'blue')
#chromosome16
plot(x=1, y = 1, type = 'n', xaxt="n", xlim = c(0, 1531933), ylim = c(-0.5, 0.5), xlab="", bty = 'n', main = paste(output, 'chr16', sep = ': '))
segments(0,0,948066,0)
chr16x <- vector()
chr16y <- vector()
for(i in 1:length(allslopes$genes)){
if(substring(allslopes[i,1],2,2) == 'P'){
# if(allslopes[i,6] > 3){
# if(allslopes[i,4] < 0.1){
errbar(allslopes[i,2], allslopes[i,3], allslopes[i,3]+allslopes[i,4]*2, allslopes[i,3]-allslopes[i,4]*2, add = T, pch = '', xaxt = 'n', cap = 0)
points(allslopes[i,2], allslopes[i,3], type = 'p', cex=0.7, col= "black", bg="lightskyblue", pch=21, xaxt="n", xlim = c(0, 1531933), ylim = c(-0.9, 0.5), xlab="", bty = 'n')
chr16x <- append(chr16x, allslopes[i,2])
chr16y <- append(chr16y, allslopes[i,3])
# }
# }
}
}
# lines(chr16x, chr16y, col = 'blue')
# segments(300000,0,1231933,0, col = 'orange', lwd = 3)
# segments(1154216,0,1161320,0, col = 'orange', lwd = 5)
points(x = c(555957), y = c(0), pch = 15, col = 'red')
# segments(1443403,0,1441433,0,col = 'red', lwd = 5)
# dev.off()
}
plot1 <- genome(inputdir=args[2], inputfile=paste('/',args[3],"_slopes_mean_norm.csv", sep = ''), scriptdir = args[1],output=paste('/',args[3],"_plot_by_chr"))
plot1 <- genome(inputdir=args[2], inputfile=paste('/',args[4],"_slopes_mean_norm.csv", sep = ''), scriptdir = args[1],output=paste('/',args[4],"_plot_by_chr"))