Hello,

I found here the below code for for ploting genes density along the chromosomes. Here it is described how to do ploting SNP density along the chromosomes.

How is it possible to combine the two codes together in order to be able to plot SNPs and genes density along the chromosomes (maybe with two trasparent colours)?

# check if ggplot2 is installed, if so, load it,
# if not, install and load it
if("ggplot2" %in% rownames(installed.packages())){
    library(ggplot2)
} else {
    install.packages("ggplot2")
    library(ggplot2)
}

# import a text file with gene positions
# columns should be: chr, position (no end or gene name required)
genes <- read.table("genes.txt",sep="\t",header=T)

# make sure the chromosomes are ordered in the way you want
# them to appear in the plot
genes$chr <- with(genes, factor(chr, levels=paste("chr",c(1:22,"X","Y"),sep=""), ordered=TRUE))

# make a density plot of genes over the provided chromosomes (or scaffolds ...)
plottedGenes <- ggplot(genes) + geom_histogram(aes(x=pos),binwidth=1000000) + facet_wrap(~chr,ncol=2) + ggtitle("RefSeq genes density over human genome 19") + xlab("Genomic position (bins 1 Mb)") + ylab("Number of genes")

# save it to an image
png("genes.png",width=1000,height=1500)
print(plottedGenes)
dev.off()

Thank you in advance.

Mic