Layout & Positioning

The Layout panel assigns spatial positions to nodes. It exposes the full graph drawing toolbox — force-directed, spectral, geometric, hierarchical, and Graphviz algorithms — in both 2D and 3D variants.

The parent panel shows a quick status card with the node and edge counts of the active graph and, for large graphs, a recommendation to avoid slow algorithms (e.g. it warns when Spring/Spring 3D is selected on graphs above 1,000 or 10,000 nodes and suggests DrL, Yifan Hu, or LGL instead). If no graph is loaded, it prompts you to create one in the Data panel first.

Subpanel — Algorithm Selection

Choose the layout algorithm. An Algorithm Info card reports its dimensionality (2D/3D), an indicative speed rating, and the use case it is best suited for.

Available algorithms

Algorithm Dim Speed Best for
Random 3D Instant Quick test, initial positions
Grid 2D Instant Regular 2D arrangement
Sphere 3D Instant Spherical distribution
Spiral 3D 3D Instant Temporal/sequential data
Helix 3D Instant DNA-like, paired data
Cube 3D Instant Bounded 3D space
Spectral 3D 3D Fast Community structure
MDS 3D 3D Medium Distance preservation
Hierarchical 3D 3D Fast Tree-like structures
Bipartite 3D 3D Fast Two-set graphs
Yifan Hu (sfdp) 3D Fast Large graphs, best quality
igraph DrL 3D Very fast Massive graphs (100k+)
igraph Fruchterman–Reingold 3D Fast General purpose
igraph Kamada–Kawai 3D Medium Reproducible layouts
igraph LGL 3D Fast Very large sparse graphs
igraph Davidson–Harel 2D Medium High-quality optimization
igraph Graphopt 2D Fast Energy minimization
ForceAtlas2 2D Medium Gephi compatibility
Spring 2D Slow Classic 2D (NetworkX)
Spring 3D 3D Very slow Classic 3D (NetworkX)
Sugiyama 2D Fast DAGs, workflows, processes
Circular Hierarchy 2D Fast Hierarchies from roots
Graphviz dot/neato/fdp/sfdp/twopi/circo/osage/patchwork 2D* Fast Canonical Graphviz drawings

* The Graphviz neato, fdp, and sfdp engines support native 3D via scigraphs-utils 0.1.1 or newer.

Subpanel — Quick Settings

A minimal one-click path: set the global Scale and press Apply Layout Now to compute the layout once with default parameters.

Subpanel — Interactive Mode

Gephi-style real-time layout that computes positions iteratively over the timeline so you can watch convergence and stop at any point.

Control Description
Timeline Reports the current frame range used for the animation.
Iterations/Frame Number of solver iterations performed per frame.
Speed (sec/frame) Wall-clock pacing of the animation.
Auto-Stop Energy Energy threshold below which the layout stops automatically (convergence).
Live Update Updates the viewport every frame.
Show Forces Visualizes the forces acting on nodes.
Start Execution Begins the iterative layout.
Reset Restarts from the initial positions.
Bake to Animation Stores positions as keyframes for playback/render.

A Current Status box reports the iteration count and energy, and indicates when the layout is converging.

Tip

Algorithm-specific parameters (next subpanel) are honoured in Interactive Mode. The one-click Apply Layout Now uses default values.

Subpanel — Algorithm Parameters

Note

When it appears: only for algorithms that expose custom parameters (Spring, ForceAtlas2, the igraph family, Yifan Hu, and the Graphviz engines).

The fields shown adapt to the selected algorithm. The most important groups:

Spring (NetworkX) — iterations; force dynamics (repulsion, attraction, gravity, edge distance); convergence control (initial temperature, cooling factor).

ForceAtlas2 — scaling ratio, gravity, strong gravity, lin-log mode, Barnes–Hut optimization (with theta), jitter tolerance, edge-weight influence.

Fruchterman–Reingold — start temperature, cool exponent, max delta, area, repulse radius.

Kamada–Kawai — max iterations, epsilon, KK constant.

DrL — global edge-cut plus per-phase parameters (Init, Liquid, Expansion, Cooldown, Crunch, Simmer), each with iterations, temperature, attraction, and damping multiplier.

LGL — max iterations, max delta, area, cool exponent, repulse radius, cell size.

Davidson–Harel — max/fine iterations, cooling factor, and weights (node distance, border, edge lengths, edge crossings, node–edge distance).

Graphopt — iterations, node charge, node mass, spring length, spring constant, max simulated-annealing movement.

Yifan Hu (sfdp) — dimension mode (2D, 3D, or 2D+Z with a Z-depth method and scale), force parameters (K, repulsive force, max iterations), quality controls (smoothing, quadtree, multilevel levels, beautify), and overlap removal (with prism scaling). Plus pass-through advanced Graphviz attributes.

Graphviz engines — engine-specific options (e.g. dot rank direction and separations; neato mode/model/start/maxiter; twopi root and rank separation; circo minimum distance; osage packing) and three pass-through fields for raw graph/node/edge attributes.

Subpanel — Network Splitter 3D

Decomposes any computed layout into distinct Z-layers, separating nodes along the vertical axis by a chosen criterion. Apply it after a 2D/3D layout.

Control Description
Split Criterion Community, Attribute, Degree, Centrality, or connected component. Each exposes its own options (community algorithm + resolution; attribute name; degree/centrality bins).
Layer Height Vertical spacing between layers.
Base Z Z offset of the first layer.
Order Ordering of layers along Z.
Preserve XY Positions Keeps the original planar coordinates within each layer.
Center Each Layer Recentres nodes within their layer.
Scale by Layer Size Scales layers according to their node count.
Inter-Layer Edges Controls how edges spanning layers are drawn.
Split Network Performs the split; a status line reports the resulting layer count and criterion.
Reset Restores the unsplit layout.

Typical workflow

  1. In Algorithm Selection, pick an algorithm appropriate to your graph size and structure (consult the table above).
  2. Tune values in Algorithm Parameters if needed.
  3. Either press Apply Layout Now (Quick Settings) for a one-shot result, or use Interactive Mode to watch convergence and bake an animation.
  4. Optionally apply Network Splitter 3D to stratify communities or metrics into Z-layers.
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