Need help with R script to edit x-axis of snp density plot

Question

[deepti1rao]

I am using the following code to plot Chromosome-wide SNP densities. It generates the attached output, such that X-axis for all the chromosomes is of the same length. It can be misleading, as it appears as if the right ends of some (reads short) chromosomes is totally devoid of snps. Can I have shorter X-axes for the shorter chromosomes?? Please help me edit the script to suit my needs

snps<-read.table("no_C_no_M_homo_snps.Galaxy12-[Cut_on_data_10].tabular",sep="\t",header=F,blank.lines.skip=TRUE,
                 comment.char = "#")
colnames(snps)<-c("chr","start","id","refallele","altallele","qual",
                  +                   "filter","info","format")
summary(snps)
goodChrOrder <- c(paste("Chr",c(1:12),sep=""))
snps$chr <- factor(snps$chr,levels=goodChrOrder)

Plot the densities of snps in the bed file for each chr seperately

library(ggplot2)
snpDensity<-ggplot(snps) + 
geom_histogram(aes(x=start),binwidth=1e4,color="brown4") + # pick a binwidth that is not too small 
    +     facet_wrap(~ chr,ncol=2) + # seperate plots for each chr, x-scales can differ from chr to chr
    +     ggtitle("Chromosome-wise homozygous snp distribution") + theme(plot.title = element_text(hjust = 0.5)) +
xlab("Genomic location (bp)") + 
ylab("SNP density")  
p <- snpDensity
p.labs <- p + labs(title = "Chromosome-wise homozygous SNP distribution", x = "Genomic location(bp)", y = "SNP density")
p.labs
y.6.text <- element_text(size = 6)
## for y axis only
p.labs + theme(axis.text.y = y.6.text)

[cpad0112]

Free scale the axis @op

[Russ]

"scales: Are scales shared across all facets (the default, "fixed"), or do they vary across rows ("free_x"), columns ("free_y"), or both rows and columns ("free")"

So try adding a scales="free_x" argument to your facet_wrap function.

[cpad0112]

some example data would help @OP

[deepti1rao]

Can anyone help with this?

[Ram]

You may wish to reconsider your plot type, as you cannot use a facet when your common axis (chr position) is dissimilar in scale This is possible. See: C: Need help with R script to edit x-axis of snp density plot

I'd also recommend you try generating separate plots + arranging them into a grid using gridExtra::arrangeGrob or the cowplot package.

[xia010]

I have same problem here. Did you figure out how to get shorter x-axis for smaller chromosomes? Thanks!

Answer 1

[bernatgel]

I would recommend using a tool specific for plotting data on the genome such as karyoploteR. With this kind of tools, you'll get all your chromosomes into scale for free.

The code would be something like this (untested):

library(karyoploteR)

snps<-read.table("no_C_no_M_homo_snps.Galaxy12-[Cut_on_data_10].tabular",sep="\t",header=F,blank.lines.skip=TRUE,
             comment.char = "#")
colnames(snps)<-c("chr","start","id","refallele","altallele","qual", "filter","info","format")

#make a GRanges with your data (we need to repeat column 2 as start and end for this to work)
snps.gr <- toGRanges(snps[,c(1,2,2)])

#Begin plotting
kp <- plotKaryotype(genome="hg19") #<- use the genome you need, if not human
kp <- kpPlotDensity(kp, data=snps.gr, col="blue")

#To add the axis, first get the max density value
max.density <- kp$latest.plot$computed.values$max.density
kpAxis(kp, ymin=0, ymax=max.density, numticks = 3)

And that's it. With this you should get something like this

You can customize it in many ways (change colors, etc...) or represent only some of the chromosomes or even zoom to specific regions.

You can find more info on that in the karyoploteR tutorial page and specifically in the kpPlotDensity page or the Gene Density example.

Hope this helps