Visualize a genome

Question

[ahmad]

Hi,

I have a set of genomic coordinates (e.g., gene identifier, start position, end position). For each gene identifier, I have quantitative values which describe some measurement of interest. I'm trying to plot the genome where each genomic segment is colored according to the quantitative value it has. An example is the following:

"Gene id" "Start position" "End position" "Quantitative value"
..
..
gi_x    15830    16450   10
gi_y    16552    17307   21
..
..

Does anyone have recommendations about an R tool I can use to visualize such data?

Answer 1

[gtho123]

It sounds like you want to construct a karyogram.

You can do this with an R package called ggbio. See section 4.3 in the vignette or this demo in the docs. Basically you plot the chromosomes and fill them in based on the quantitative value you assign to it.