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docs/src/introduction_to_catalyst/introduction_to_catalyst.md

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@@ -92,7 +92,7 @@ g = plot_network(rn)
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```
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The network graph shows a variety of information, representing each species as a
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blue node, and each reaction as an orange dot. Black arrows from species to
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blue node, and each reaction as an green node. Black arrows from species to
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reactions indicate reactants, and are labelled with their input stoichiometry.
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Similarly, black arrows from reactions to species indicate products, and are
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labelled with their output stoichiometry. In contrast, red arrows from a species

docs/src/model_creation/model_visualisation.md

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@@ -76,9 +76,12 @@ Finally, a [network's reaction complexes](@ref network_analysis_reaction_complex
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```@example visualisation_graphs
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plot_complexes(brusselator)
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```
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Here, reaction complexes are displayed as blue nodes, and reactions between complexes are displayed as black arrows. Edges are labeled with their rate expressions.
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Here, reaction complexes are displayed as blue nodes, and reactions between complexes are displayed as black arrows. Red arrows indicate that the rate constantof a reaction has a species-dependence. Edges can be optionally labeled with their rate expressions by calling with the option `show_rate_labels`.
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```@example visualisation_graphs
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plot_complexes(brusselator, show_rate_labels = true)
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```
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Makie graphs can be made to be interactive, allowing one to drag nodes and edges. To do this, we retrieve the axis from the GraphMakie plot, and then register the interactions. Note that this can only be done if `GLMakie` is the installed Makie backend. See the [GraphMakie docs](https://graph.makie.org/stable/#Predefined-Interactions) for more information.
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Makie graphs can be made to be interactive, allowing one to drag nodes and edges. To do this, we retrieve the axis from the GraphMakie plot, and then register the interactions. **Note that this can only be done if `GLMakie` is the installed Makie backend. See the [GraphMakie docs](https://graph.makie.org/stable/#Predefined-Interactions) for more information about the types of interactions one can register.** Below is a non-interactive code example:
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```julia
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using GLMakie

ext/CatalystGraphMakieExtension/rn_graph_plot.jl

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Notes:
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- Black arrows from complexes to complexes indicate reactions whose rate is a
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parameter or a `Number`. i.e. `k, A --> B`.
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- Red arrows from complexes to complexes indicate reactions whose rate
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- Red arrows from complexes to complexes indicate reactions whose rate constants
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depends on species. i.e. `k*C, A --> B` for `C` a species.
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- The `show_rate_labels` keyword, if set to `true`, will annotate each edge
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with the rate constant for the reaction.

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