# Reaction Path Diagrams

(jl-type-reactionpathdiagram)=
::::{describe} ReactionPathDiagram(gas::Solution, element::AbstractString)
Reaction-path diagram tracing the flow of a chemical `element` (e.g. `"C"`,
`"H"`, `"O"`, `"N"`) through the reaction network of `gas` at its current state.

Set options (see [`set_threshold!`](#jl-function-set-threshold-bang), [`set_flow_type!`](#jl-function-set-flow-type-bang), ...), then
call [`build!`](#jl-function-build-bang) and retrieve the result with [`get_dot`](#jl-function-get-dot) (Graphviz),
[`get_data`](#jl-function-get-data) or [`get_log`](#jl-function-get-log).

```julia
gas = Solution("gri30.yaml")
set_TPX!(gas, 2000.0, one_atm, "CH4:1, O2:2, N2:7.52")
d = ReactionPathDiagram(gas, "C")
set_threshold!(d, 0.01)
set_flow_type!(d, "NetFlow")
build!(d)
print(get_dot(d))
```
::::

(jl-function-build-bang)=
::::{describe} build!(d::ReactionPathDiagram)
Build (or rebuild) the diagram from the current state of the owning Solution.
Call after setting options and before retrieving output.
::::

(jl-function-get-dot)=
::::{describe} get_dot(d::ReactionPathDiagram)
Graphviz `dot` description of the diagram (call [`build!`](#jl-function-build-bang) first).
::::

(jl-function-get-data)=
::::{describe} get_data(d::ReactionPathDiagram)
Raw flow data underlying the diagram (call [`build!`](#jl-function-build-bang) first).
::::

(jl-function-get-log)=
::::{describe} get_log(d::ReactionPathDiagram)
Diagnostic log accumulated while building the diagram.
::::

(jl-function-normal-threshold)=
::::{describe} normal_threshold(d::ReactionPathDiagram)
Maximum relative flux for dashed lines.
::::

(jl-function-arrow-width)=
::::{describe} arrow_width(d::ReactionPathDiagram)
Arrow width; if negative, arrows scale with the flux value instead.
::::

(jl-function-scale)=
::::{describe} scale(d::ReactionPathDiagram)
Scaling factor for the fluxes; -1 normalizes by the maximum net flux.
::::

(jl-function-threshold)=
::::{describe} threshold(d::ReactionPathDiagram)
Minimum relative flux value that will be plotted.
::::

(jl-function-label-threshold)=
::::{describe} label_threshold(d::ReactionPathDiagram)
Minimum relative flux for labels.
::::

(jl-function-bold-threshold)=
::::{describe} bold_threshold(d::ReactionPathDiagram)
Minimum relative flux for bold lines.
::::

(jl-function-set-scale-bang)=
::::{describe} set_scale!(d::ReactionPathDiagram, v::Real)
Set [`scale`](#jl-function-scale).
::::

(jl-function-set-threshold-bang)=
::::{describe} set_threshold!(d::ReactionPathDiagram, v::Real)
Set [`threshold`](#jl-function-threshold).
::::

(jl-function-set-label-threshold-bang)=
::::{describe} set_label_threshold!(d::ReactionPathDiagram, v::Real)
Set [`label_threshold`](#jl-function-label-threshold).
::::

(jl-function-set-bold-threshold-bang)=
::::{describe} set_bold_threshold!(d::ReactionPathDiagram, v::Real)
Set [`bold_threshold`](#jl-function-bold-threshold).
::::

(jl-function-set-normal-threshold-bang)=
::::{describe} set_normal_threshold!(d::ReactionPathDiagram, v::Real)
Set [`normal_threshold`](#jl-function-normal-threshold).
::::

(jl-function-set-arrow-width-bang)=
::::{describe} set_arrow_width!(d::ReactionPathDiagram, v::Real)
Set [`arrow_width`](#jl-function-arrow-width).
::::

(jl-function-font)=
::::{describe} font(d::ReactionPathDiagram)
Font used for the diagram.
::::

(jl-function-dot-options)=
::::{describe} dot_options(d::ReactionPathDiagram)
Options passed through to the `dot` program.
::::

(jl-function-flow-type)=
::::{describe} flow_type(d::ReactionPathDiagram)
Way flows are drawn: `"NetFlow"` or `"OneWayFlow"`.
::::

(jl-function-bold-color)=
::::{describe} bold_color(d::ReactionPathDiagram)
Color for bold lines.
::::

(jl-function-normal-color)=
::::{describe} normal_color(d::ReactionPathDiagram)
Color for normal-weight lines.
::::

(jl-function-dashed-color)=
::::{describe} dashed_color(d::ReactionPathDiagram)
Color for dashed lines.
::::

(jl-function-title)=
::::{describe} title(d::ReactionPathDiagram)
Reaction path diagram title.
::::

(jl-function-set-title-bang)=
::::{describe} set_title!(d::ReactionPathDiagram, v::AbstractString)
Set [`title`](#jl-function-title).
::::

(jl-function-set-bold-color-bang)=
::::{describe} set_bold_color!(d::ReactionPathDiagram, v::AbstractString)
Set [`bold_color`](#jl-function-bold-color).
::::

(jl-function-set-dot-options-bang)=
::::{describe} set_dot_options!(d::ReactionPathDiagram, v::AbstractString)
Set [`dot_options`](#jl-function-dot-options).
::::

(jl-function-set-flow-type-bang)=
::::{describe} set_flow_type!(d::ReactionPathDiagram, v::AbstractString)
Set [`flow_type`](#jl-function-flow-type).
::::

(jl-function-set-font-bang)=
::::{describe} set_font!(d::ReactionPathDiagram, v::AbstractString)
Set [`font`](#jl-function-font).
::::

(jl-function-set-normal-color-bang)=
::::{describe} set_normal_color!(d::ReactionPathDiagram, v::AbstractString)
Set [`normal_color`](#jl-function-normal-color).
::::

(jl-function-set-dashed-color-bang)=
::::{describe} set_dashed_color!(d::ReactionPathDiagram, v::AbstractString)
Set [`dashed_color`](#jl-function-dashed-color).
::::

(jl-function-show-details)=
::::{describe} show_details(d::ReactionPathDiagram)
Whether reaction details are shown as edge labels.
::::

(jl-function-set-show-details-bang)=
::::{describe} set_show_details!(d::ReactionPathDiagram, v::Bool)
Enable or disable showing reaction details as edge labels.
::::

(jl-function-display-only-bang)=
::::{describe} display_only!(d::ReactionPathDiagram, species_index)
Restrict the diagram to flows into/out of a single species (1-based index), or
pass `:all` (or a negative index) to show all species again.
::::