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# ggplot-windows-multi.R -- Plot number of each windows along chromosomes using ggplot, support multi-sample input.

#

#

# Author: Nowind

# Created: 2013-07-10

# Updated: 2014-11-29

# Version: 1.0.0

#

# Change logs:

# Version 1.0.0 14/11/29: The initial version.

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library(lsr)

library(reshape2)

library(ggplot2)

library(grid)

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## plot distributions of markers

varfile <- commandArgs(TRUE)[1]

out_tiff <- commandArgs(TRUE)[2]

variants <- as.data.frame(read.table(varfile, header=T, sep="\t"))

chrom_num <- length(unique(variants$chrom))

out_height <- chrom_num * 600

tiff(out_tiff, width=4800, height=out_height, units='px', res=600, compression='lzw', bg='transparent')

variants_melted <- melt(variants, id.vars=c("chrom", "interval", "bin"))

ggplot(variants_melted, aes(x=bin, y=value, colour=variable, group=variable)) +

geom_line() +

xlab("Windows(x500kbp)") +

ylab("Number of Variants") +

scale_colour_hue(name="variable",

breaks=unique(variants_melted$variable),

labels=unique(variants_melted$variable),

l=40) +

theme_bw() +

theme(legend.justification=c(1,0), legend.position=c(1,0)) +

facet_grid(chrom ~ ., scales="free_y")

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warnings()