Adding ggplot2 chromosome position variable

Question

[rbronste]

Hi pretty basic question, but I have a data.frame that looks as follows:

  chrom   start    stop frag        dev span
1  chr1 3466334 3466335   60 0.09543313 0.94
2  chr1 4970790 4970791   51 0.08546289 1.00
3  chr1 5022767 5022768   27 0.45680640 0.20
4  chr1 5022807 5022808   34 0.35155312 0.20
5  chr1 5022904 5022905   45 0.12787640 0.20
6  chr1 5023063 5023064   29 0.26792518 0.20

I am trying to do a scatter plot at specific genomic locations, just not sure how to limit it to the right chromosome, here is my ggplot2 command:

my_data %>% ggplot() + geom_point(aes(x = start, y = frag)) + scale_y_continuous(limits=c(0,80)) + xlim(109005904, 109017426) + xlab("Genomic Position") + geom_smooth(aes(x = start, y = frag), method="loess", span=.66, color = "red", fill = "black") + theme_bw()

Thanks!

Answer 1

[zx8754]

Maybe:

my_data %>% filter(chrom == "chr1") %>% ggplot() + ...

Answer 2

[bernatgel]

Hi rbonste

If you are wiling to move out of the ggplot space, you could use the Bioconductor package karyoploteR(https://bioconductor.org/packages/karyoploteR/), a tool specifically designed for the type of work you need, to plot data on genomes.

To use it you'll need to: first, create an empty (with no data, only the ideograms) karyoplot using plotKaryotype and them use kpPoints to add your data.

kp <- plotKaryotype("hg19")
kpAxis(kp, ymin = 0, ymax=100)
kpPoints(kp, my.data, y=my.data$frag, ymin=0, ymax=100)

And you'd get an image like this one

If you want to plot the data in a single chromosome you can select it in the first function call with chromosomes="chr1"

kp <- plotKaryotype("hg19", chromosomes = "chr1", main="Chromosome 1")
kpAxis(kp, ymin = 0, ymax=100)
kpPoints(kp, my.data, y=my.data$frag, ymin=0, ymax=100)

In addition, you can add additional information such as a LOESS fit or other data types, or customize the font sizes or point colors to get to this

kp <- plotKaryotype("hg19", chromosomes = "chr1", main="Chromosome 1", cex=2)
kpAxis(kp, ymin = 0, ymax=100, cex=1.8)
point.colors <- colByValue(my.data$frag, colors = c("green", "black","red"), min = 40, max=80)
kpPoints(kp, my.data, y=my.data$frag, ymin=0, ymax=100, col=point.colors, cex=1.5)
kpPlotLoess(kp, my.data, y=my.data$frag, ymin=0, ymax=100, ci.col = transparent("orchid"))

You can find more information on how to use karyoploteR in the tutorial page.