Plotting isoforms

After Parsing GENCODE, it is possible to plot isoform bodies. We can focus on NRXN1 gene as our initial example. GeneticsMakie.plotisoforms! returns genomic coordinates for the gene of interest so that an appropriate label can be passed onto GeneticsMakie.labelgenome. NRXN1 gene has many isoforms as we see below, and even more isoforms are likely to be discovered in the future. For this reason, plotting isoforms of multiple genes is not available.

using Pkg
Pkg.add(["GeneticsMakie", "CairoMakie", "DataFrames", "Arrow"])

using GeneticsMakie, CairoMakie, DataFrames, Arrow
url = "https://ftp.ebi.ac.uk/pub/databases/gencode/Gencode_human/release_39/GRCh37_mapping/gencode.v39lift37.annotation.gtf.gz"
gencode = Arrow.Table("data/gencode/$(splitext(basename(url))[1]).arrow")|> DataFrame

isdir("figs") || mkdir("figs")
set_theme!(font = "Arial")

gene = "NRXN1"
f = Figure(size = (306, 792))
ax = Axis(f[1, 1])
rs, chr, range1, range2 = GeneticsMakie.plotisoforms!(ax, gene, gencode; height = 0.1)
GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, range1, range2)
rowsize!(f.layout, 1, rs)
resize_to_layout!(f)
f

To save some space, we can plot the isoform labels on the left by using the text keyword argument.

f = Figure(size = (306, 792))
ax = Axis(f[1, 1])
rs, chr, range1, range2 = GeneticsMakie.plotisoforms!(ax, gene, gencode; height = 0.1, text = :l)
GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, range1, range2)
rowsize!(f.layout, 1, rs)
resize_to_layout!(f)
f

We can change the color of isoforms and text using the isoformcolor and textcolor keyword arguments, respectively. We look at a different gene, GRIN2A.

gene = "GRIN2A"
f = Figure(size = (306, 792))
ax = Axis(f[1, 1])
rs, chr, range1, range2 = GeneticsMakie.plotisoforms!(ax, gene, gencode; isoformcolor = :forestgreen, height = 0.1)
GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, range1, range2)
rowsize!(f.layout, 1, rs)
resize_to_layout!(f)
f

We can change the order of isoforms by using the orderby keyword argument.

f = Figure(size = (306, 792))
ax = Axis(f[1, 1])
rs, chr, range1, range2 = GeneticsMakie.plotisoforms!(ax, gene, gencode; orderby = ["ENST00000675189", "ENST00000463531"], isoformcolor = :forestgreen, height = 0.1)
GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, range1, range2)
rowsize!(f.layout, 1, rs)
resize_to_layout!(f)
f

f = Figure(size = (306, 792))
ax = Axis(f[1, 1])
rs, chr, range1, range2 = GeneticsMakie.plotisoforms!(ax, gene, gencode; orderby = ["ENST00000675189", "ENST00000463531"], 
    highlight = (["ENST00000675398", "ENST00000562109"], fill(:brown3, 2)), isoformcolor = :forestgreen, height = 0.1)
GeneticsMakie.labelgenome(f[1, 1, Bottom()], chr, range1, range2)
rowsize!(f.layout, 1, rs)
resize_to_layout!(f)
f