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repostatus-img Escher Downloads

This package implements a Makie recipe called escherplot that plots maps of metabolic models resembling its namesake GUI. Its primary purpose is to facilitate the generation of high quality metabolic maps from within Julia.

Plot the core metabolism of E. coli with fluxes

Here COBREXA.jl is used to estimate fluxes of reactions using the metabolic model of iJO1366, an E. coli metabolic model. The associated map can be downloaded from the Escher website. If you want to run these examples, please download the associated models and maps, and place them in the datadirectory.

using Escher, CairoMakie, ColorSchemes
using COBREXA, Tulip
using Clustering

# use COBREXA to generate a flux distribution using the associated model
model = load_model(joinpath(pkgdir(Escher), "data", "iJO1366-model.json"))
#=
Bin fluxes for display purposes - assigning colors to edges needs to be done
manually. The binning uses kmeans clustering on logged fluxes due to the large
differences between fluxes.
=#
logged_fluxes = log.(abs.(flux_balance_analysis_vec(model, Tulip.Optimizer)) .+ 1e-8)
clusters = kmeans(logged_fluxes', 9)
centers = Dict(j=>i for (i, j) in enumerate(sortperm(clusters.centers'[:])))
order = [centers[i] for i in assignments(clusters)]

rc = Dict(rid => ColorSchemes.RdYlBu_9[10-k] # map reaction id to color
    for (rid, k) in zip(reactions(model), order))

f = Figure(resolution = (1200, 800));
ax = Axis(f[1, 1]);
escherplot!(
    ax,
    joinpath(pkgdir(Escher), "data", "iJO1366-map.json");
    reaction_edge_colors = rc,
)
hidexdecorations!(ax)
hideydecorations!(ax)
f

Overlay even more data with colors and node/edge sizes

The previous example only highlighted reactions according to their fluxes. Escher.jl also allows you to control the size and colors of the nodes, as well as the size of the reaction edges. This time we will use a smaller "core" model with its associated map.

using Escher, CairoMakie, ColorSchemes
using COBREXA, Tulip

model = load_model(joinpath(pkgdir(Escher), "data", "core-model.json"))
sol = flux_balance_analysis_dict(model, Tulip.Optimizer)

# Find min and max absolute fluxes for normalization
maxflux = maximum(abs.(values(sol)))
minflux = minimum(abs.(values(sol)))

# Scale width of reaction edges to fluxes
width_interp(x) = 2 + 5 * (abs(x) - minflux) / (maxflux - minflux) # widths between 2 and 5
re = Dict(k => width_interp(v) for (k, v) in sol) # map reaction id to reaction edge width

# Scale color of reaction edges to fluxes (manually binned)
color_interp(x) = begin
    normed_x = (abs(x) - minflux) / (maxflux - minflux)
    if 0 <= normed_x < 0.01
        ColorSchemes.RdYlBu_4[4]
    elseif 0.01 <= normed_x < 0.25
        ColorSchemes.RdYlBu_4[3]
    elseif 0.25 <= normed_x < 0.5
        ColorSchemes.RdYlBu_4[2]
    else
        ColorSchemes.RdYlBu_4[1]
    end
end
rc = Dict(k => color_interp(v) for (k, v) in sol) # map reaction id to reaction edge color

# metabolite node colors
mc = Dict(
    k => ColorSchemes.:Dark2_7[v] for
    (k, v) in zip(metabolites(model), rand(1:7, n_metabolites(model)))
)

# metabolite node sizes
ms = Dict(k => v for (k, v) in zip(metabolites(model), rand(3:10, n_metabolites(model))))

# Normal Makie plotting features all work (escherplot is a full recipe)
f = Figure(resolution = (1200, 800));
ax = Axis(f[1, 1]);
escherplot!(
    ax,
    joinpath(pkgdir(Escher), "data", "core-map.json");
    reaction_edge_widths = re,
    reaction_edge_colors = rc,
    metabolite_node_colors = mc,
    metabolite_node_sizes = ms,
)
hidexdecorations!(ax)
hideydecorations!(ax)
f

This results in:

Attributes

The escherplot recipe exposes a number of custom attributes that can be used to modify the basic metabolic map figure. The names are all self-explanatory but some comments are provided for clarity.

metabolite_identifier = "bigg_id"
metabolite_show_text = false
metabolite_text_size = 4
metabolite_primary_node_size = 5 # fallback size
metabolite_secondary_node_size = 3 # fallback size
metabolite_node_sizes = Dict{String,Any}()
metabolite_node_colors = Dict{String,Any}()
metabolite_node_color = :black # fallback color
metabolite_text_color = :black
reaction_identifier = "bigg_id"
reaction_show_text = false
reaction_show_name_instead_of_id = false
reaction_text_size = 4
reaction_text_color = :black
reaction_edge_colors = Dict{String,Any}() # actual color
reaction_edge_color = :black # fallback color
reaction_edge_widths = Dict{String,Any}() # actual edge width
reaction_edge_width = 2.0 # fallback width
reaction_arrow_size = 6
reaction_arrow_head_offset_fraction = 0.5 # between 0 and 1
reaction_directions = Dict{String,Tuple{Dict{String,Number},Symbol}}() # rid => (reaction stoichiometry, :f or :r)
annotation_show_text = false
annotation_text_color = :black
annotation_text_size = 12

Note, if reaction_edge_colors or reaction_edge_widths are supplied but missing an id that is present in the map, the associated edge will be dotted.

More examples

These examples all use the same data as the second example, but demonstrate the use of different attributes. For brevity it is assumed that the functions below are inserted as indicated here:

f = Figure(resolution = (1200, 800));
ax = Axis(f[1, 1]);
###### PLOT FUNCTION
hidexdecorations!(ax)
hideydecorations!(ax)
f

Basic plot

Basic plot showing only the edges (reactions) and nodes (metabolites).

escherplot!(ax, joinpath(pkgdir(Escher), "data", "core-map.json"))

Adding labels

Basic plot showing the labels of the nodes and reactions.

escherplot!(
    ax,
    joinpath(pkgdir(Escher), "data", "core-map.json");
    metabolite_show_text=true,
    reaction_show_text=true,
    annotation_show_text = true,
)

Missing data

If incomplete reaction data (edge colors or widths) are supplied the missing reaction edges are dotted.

rc = Dict("FBA" => ColorSchemes.RdYlBu_4[4],
    "PFK" => ColorSchemes.RdYlBu_4[3],
    "PEP" => ColorSchemes.RdYlBu_4[2],
    "PYK" => ColorSchemes.RdYlBu_4[1])
escherplot!(
    ax,
    joinpath(pkgdir(Escher), "data", "core-map.json");
    reaction_edge_colors = rc,
)

Reaction directions

It is also possible to add direction arrows to reactions through the reaction_directions attribute. It is a dictionary, which maps reaction ids to reaction stoichiometry of the model used to simulate fluxes, and a symbol :forward, :backward, :bidirectional. Arrows are then placed on reactions in the direction relative to the supplied stoichiometry of the reaction.

rd = Dict(
    "PGM" => (Dict("3pg_c" => 1, "2pg_c" => -1), :backward),
    "PYK" => (Dict("pep_c" => -1, "adp_c" => -1, "h_c" => -1.0, "atp_c" => 1.0, "pyr_c" => 1), :forward),
    "ENO" => (Dict("2pg_c" => 1, "pep_c" => -1, "h2o_c" => -1), :bidirectional),
)

escherplot!(
    ax,
    joinpath(pkgdir(Escher), "data", "core-map.json");
    reaction_directions = rd,
    reaction_arrow_size = 12,
    reaction_show_text = true,
)
hidexdecorations!(ax)
hideydecorations!(ax)

Map dimensions

Finally, the original map dimensions can be queried by calling get_resolution.

h, w, x, y = get_resolution(joinpath(pkgdir(Escher), "data", "core-map.json"))
f = Figure(resolution = (x, y))
...