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add an example for objective_envelope #441

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merged 4 commits into from
Aug 16, 2021
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add an example for objective_envelope #441

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5bb05b2
add an example for objective_envelope
exaexa Aug 16, 2021
8ed7d68
fix the docstring
exaexa Aug 16, 2021
69340c9
explain `lattice_args` a bit better
exaexa Aug 16, 2021
8a62eb6
typos
htpusa Aug 16, 2021
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38 changes: 33 additions & 5 deletions src/analysis/envelopes.jl
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Original file line number Diff line number Diff line change
Expand Up @@ -19,7 +19,7 @@ envelope_lattice(model::MetabolicModel, rids::Vector{String}; kwargs...) =

Create a lattice (list of "tick" vectors) for reactions at indexes `ridxs` in a
model. Arguments `samples`, `ranges`, and `reaction_samples` may be optionally
specified to customize the latice creation process.
specified to customize the lattice creation process.
"""
envelope_lattice(
model::MetabolicModel,
Expand All @@ -35,7 +35,7 @@ envelope_lattice(
"""
objective_envelope(model::MetabolicModel, rids::Vector{String}, args...; kwargs...)

Versioin of [`objective_envelope`](@ref) that works on string reaction IDs
Version of [`objective_envelope`](@ref) that works on string reaction IDs
instead of integer indexes.
"""
objective_envelope(model::MetabolicModel, rids::Vector{String}, args...; kwargs...) =
Expand All @@ -51,7 +51,8 @@ objective_envelope(model::MetabolicModel, rids::Vector{String}, args...; kwargs.
model::MetabolicModel,
ridxs::Vector{Int},
optimizer;
lattice = envelope_lattice(model, ridxs),
lattice_args = (),
lattice = envelope_lattice(model, ridxs; lattice_args...),
kwargs...,
)

Expand All @@ -71,15 +72,42 @@ Returns a named tuple that contains `lattice` with reference values of the
metabolites, and an N-dimensional array `values` with the computed objective
values, where N is the number of specified reactions. Because of the
increasing dimensionality, the computation gets very voluminous with increasing
length of `ridxs`.
length of `ridxs`. The `lattice` for computing the optima can be supplied in
the argument; by default it is created by [`envelope_lattice`](@ref) called on
the model and reaction indexes. Additional arguments for the call to
[`envelope_lattice`](@ref) can be optionally specified in `lattice_args`.

`kwargs` are internally forwarded to [`screen_optmodel_modifications`](@ref).

# Example
```
julia> m = load_model("test/downloaded/e_coli_core.xml");

julia> envelope = objective_envelope(m, ["R_EX_gln__L_e", "R_EX_fum_e"],
Tulip.Optimizer;
lattice_args=(samples=6,));

julia> envelope.lattice # the reaction rates for which the optima were computed
2-element Vector{Vector{Float64}}:
[0.0, 200.0, 400.0, 600.0, 800.0, 1000.0]
[0.0, 200.0, 400.0, 600.0, 800.0, 1000.0]

julia> envelope.values # the computed flux objective values for each reaction rate combination
6×6 Matrix{Float64}:
0.873922 9.25815 17.4538 19.56 20.4121 20.4121
13.0354 17.508 19.9369 21.894 22.6825 22.6825
16.6666 18.6097 20.2847 21.894 22.6825 22.6825
16.6666 18.6097 20.2847 21.894 22.6825 22.6825
16.6666 18.6097 20.2847 21.894 22.6825 22.6825
16.6666 18.6097 20.2847 21.894 22.6825 22.6825
```
"""
objective_envelope(
model::MetabolicModel,
ridxs::Vector{Int},
optimizer;
lattice = envelope_lattice(model, ridxs),
lattice_args = (),
lattice = envelope_lattice(model, ridxs; lattice_args...),
kwargs...,
) = (
lattice = collect.(lattice),
Expand Down