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Styling
ScyNet offers several options for changing the network layout, all of which can be found under Apps -> ScyNet. To run them, a network created by ScyNet needs to be selected first.
- Contextualize with Flux Data
- Apply ScyNet Layout
- Toggle Non-Cross-Fed Metabolite Visibility
- Toggle Edge Width Relative to Flux
- Toggle Zero Flux Edge Visibility
ScyNet can contextualize the edges of the community network with flux data. This can be either single value fluxes (such as from FBA) or flux ranges (such as from FVA). To read the flux values with ScyNet, they need to be supplied as tab separated files (further requirements below).
The flux vector of a single state can be visualized by providing the vector in a tab separated file. This file needs to contain two columns, called reaction_id and flux.
| reaction_id | flux |
|---|---|
| dv_TP_H2_TP_dv_External_Species | 2.983079 |
| dv_TP_Ac_TP_dv_External_Species | 5.969766 |
| dv_TP_CO2_TP_dv_External_Species | -9.046403 |
| ... | ... |
Also flux ranges can be visualized with ScyNet. For doing so, a tab separated file with three columns needs to be provided: reaction_id, min_flux, max_flux.
| reaction_id | min_flux | max_flux |
|---|---|---|
| dv_TP_H2_TP_dv_External_Species | -353.182659 | 39.428060 |
| dv_TP_Ac_TP_dv_External_Species | 3.721467 | 19.677175 |
| dv_TP_CO2_TP_dv_External_Species | -392.701304 | -0.042069 |
| ... | ... | ... |
Places all nodes into concentric circles based on node type and connection to community member nodes. This layout is automatically applied when creating a simplified community network.
Hides all metabolite nodes that are not cross-fed. If all non-cross-fed metabolite nodes are hidden, it reveals them instead. Only works if flux data is available.
Sets edge widths relative to the corresponding flux values. Running this again will set all edge widths to the default width. Only works if flux data is available.
Hides all edges with a flux value of 0. If all edges with 0 flux are hidden, it reveals them instead. Only works if flux data is available.