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

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

SNP density plot

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)
snps density chromosome r
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updated by bernatgel bernatgel • written by deepti1rao • deepti1rao

some example data would help @OP

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written by cpad0112 cpad0112

Hello deepti,

Please use the formatting bar (especially the code option) to present your post better. I've done it for you this time.
code_formatting

Thank you!

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written by lakhujanivijay lakhujanivijay

See How to add images to a Biostars post to add your images properly. You need the direct link to the image, not the link to the webpage that has the image embedded (which is what you have used here)

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written by Ram 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.

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written by Ram Ram

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

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written by xia010 • xia010

Free scale the axis @op

• 1 views • link
written by cpad0112 cpad0112

"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.

• 1 views • link
written by Russ Russ

1 answer

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

enter image description here

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

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written by bernatgel bernatgel

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