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License: MIT License
Visualization of metabolic models in Makie.
License: MIT License
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Is it possible to preserve reaction directionality when plotting metabolic models with escherplot!()
using arrows!
instead of lines!
?
Hi again,
It's been a while since I've used Escher.jl for visualizing networks and am having issues with reversible reactions only showing arrowheads in one direction. I updated to Escher.jl version v0.6.5 and was following your tutorial with the E. coli core model from Bigg/Escher. From what I remember, there was no issue the first time you implemented reaction directions, but I haven't done any regression testing.
using Escher, CairoMakie, ColorSchemes
rd = Dict(
"PGM" => (Dict("3pg_c" => 1, "2pg_c" => -1), :r),
"PYK" => (Dict("pep_c" => -1, "adp_c" => -1, "h_c" => -1.0, "atp_c" => 1.0, "pyr_c" => 1), :f)
f = Figure(resolution = (1200, 800));
ax = Axis(f[1, 1]);
escherplot!(
ax,
"/path/to/escher-map-file/e_coli_core.Core metabolism.json",
reaction_directions = rd,
reaction_arrow_size = 12,
reaction_show_text = true,
)
hidexdecorations!(ax)
hideydecorations!(ax)
The resulting plot is identical to yours with only a single arrow head for the reversible PGM reaction.
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