@graphty/layout 1.2.2 → 1.2.4

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Files changed (200) hide show
  1. package/README.md +317 -237
  2. package/dist/src/algorithms/index.d.ts +5 -0
  3. package/dist/src/algorithms/index.js +6 -0
  4. package/dist/src/algorithms/index.js.map +1 -0
  5. package/dist/src/algorithms/optimization/index.d.ts +7 -0
  6. package/dist/src/algorithms/optimization/index.js +7 -0
  7. package/dist/src/algorithms/optimization/index.js.map +1 -0
  8. package/dist/src/algorithms/optimization/kamada-kawai-solver.d.ts +32 -0
  9. package/dist/src/algorithms/optimization/kamada-kawai-solver.js +176 -0
  10. package/dist/src/algorithms/optimization/kamada-kawai-solver.js.map +1 -0
  11. package/dist/src/algorithms/optimization/lbfgs.d.ts +13 -0
  12. package/dist/src/algorithms/optimization/lbfgs.js +56 -0
  13. package/dist/src/algorithms/optimization/lbfgs.js.map +1 -0
  14. package/dist/src/algorithms/optimization/line-search.d.ts +15 -0
  15. package/dist/src/algorithms/optimization/line-search.js +37 -0
  16. package/dist/src/algorithms/optimization/line-search.js.map +1 -0
  17. package/dist/src/algorithms/optimization/types.d.ts +5 -0
  18. package/dist/src/algorithms/optimization/types.js +5 -0
  19. package/dist/src/algorithms/optimization/types.js.map +1 -0
  20. package/dist/src/algorithms/planarity/check.d.ts +17 -0
  21. package/dist/src/algorithms/planarity/check.js +30 -0
  22. package/dist/src/algorithms/planarity/check.js.map +1 -0
  23. package/dist/src/algorithms/planarity/embedding.d.ts +29 -0
  24. package/dist/src/algorithms/planarity/embedding.js +179 -0
  25. package/dist/src/algorithms/planarity/embedding.js.map +1 -0
  26. package/dist/src/algorithms/planarity/index.d.ts +7 -0
  27. package/dist/src/algorithms/planarity/index.js +8 -0
  28. package/dist/src/algorithms/planarity/index.js.map +1 -0
  29. package/dist/src/algorithms/planarity/lr-test.d.ts +15 -0
  30. package/dist/src/algorithms/planarity/lr-test.js +54 -0
  31. package/dist/src/algorithms/planarity/lr-test.js.map +1 -0
  32. package/dist/src/algorithms/planarity/special-graphs.d.ts +28 -0
  33. package/dist/src/algorithms/planarity/special-graphs.js +108 -0
  34. package/dist/src/algorithms/planarity/special-graphs.js.map +1 -0
  35. package/dist/src/generators/basic.d.ts +28 -0
  36. package/dist/src/generators/basic.js +79 -0
  37. package/dist/src/generators/basic.js.map +1 -0
  38. package/dist/src/generators/bipartite.d.ts +16 -0
  39. package/dist/src/generators/bipartite.js +40 -0
  40. package/dist/src/generators/bipartite.js.map +1 -0
  41. package/dist/src/generators/grid.d.ts +11 -0
  42. package/dist/src/generators/grid.js +37 -0
  43. package/dist/src/generators/grid.js.map +1 -0
  44. package/dist/src/generators/index.d.ts +8 -0
  45. package/dist/src/generators/index.js +9 -0
  46. package/dist/src/generators/index.js.map +1 -0
  47. package/dist/src/generators/random.d.ts +12 -0
  48. package/dist/src/generators/random.js +34 -0
  49. package/dist/src/generators/random.js.map +1 -0
  50. package/dist/src/generators/scale-free.d.ts +12 -0
  51. package/dist/src/generators/scale-free.js +62 -0
  52. package/dist/src/generators/scale-free.js.map +1 -0
  53. package/dist/src/index.d.ts +10 -0
  54. package/dist/src/index.js +15 -0
  55. package/dist/src/index.js.map +1 -0
  56. package/dist/src/layouts/basic/index.d.ts +4 -0
  57. package/dist/src/layouts/basic/index.js +5 -0
  58. package/dist/src/layouts/basic/index.js.map +1 -0
  59. package/dist/src/layouts/basic/random.d.ts +14 -0
  60. package/dist/src/layouts/basic/random.js +27 -0
  61. package/dist/src/layouts/basic/random.js.map +1 -0
  62. package/dist/src/layouts/force-directed/arf.d.ts +13 -0
  63. package/dist/src/layouts/force-directed/arf.js +103 -0
  64. package/dist/src/layouts/force-directed/arf.js.map +1 -0
  65. package/dist/src/layouts/force-directed/forceatlas2.d.ts +22 -0
  66. package/dist/src/layouts/force-directed/forceatlas2.js +322 -0
  67. package/dist/src/layouts/force-directed/forceatlas2.js.map +1 -0
  68. package/dist/src/layouts/force-directed/fruchterman-reingold.d.ts +19 -0
  69. package/dist/src/layouts/force-directed/fruchterman-reingold.js +131 -0
  70. package/dist/src/layouts/force-directed/fruchterman-reingold.js.map +1 -0
  71. package/dist/src/layouts/force-directed/index.d.ts +8 -0
  72. package/dist/src/layouts/force-directed/index.js +9 -0
  73. package/dist/src/layouts/force-directed/index.js.map +1 -0
  74. package/dist/src/layouts/force-directed/kamada-kawai.d.ts +15 -0
  75. package/dist/src/layouts/force-directed/kamada-kawai.js +87 -0
  76. package/dist/src/layouts/force-directed/kamada-kawai.js.map +1 -0
  77. package/dist/src/layouts/force-directed/spring.d.ts +19 -0
  78. package/dist/src/layouts/force-directed/spring.js +23 -0
  79. package/dist/src/layouts/force-directed/spring.js.map +1 -0
  80. package/dist/src/layouts/geometric/circular.d.ts +14 -0
  81. package/dist/src/layouts/geometric/circular.js +67 -0
  82. package/dist/src/layouts/geometric/circular.js.map +1 -0
  83. package/dist/src/layouts/geometric/index.d.ts +6 -0
  84. package/dist/src/layouts/geometric/index.js +7 -0
  85. package/dist/src/layouts/geometric/index.js.map +1 -0
  86. package/dist/src/layouts/geometric/shell.d.ts +15 -0
  87. package/dist/src/layouts/geometric/shell.js +67 -0
  88. package/dist/src/layouts/geometric/shell.js.map +1 -0
  89. package/dist/src/layouts/geometric/spiral.d.ts +16 -0
  90. package/dist/src/layouts/geometric/spiral.js +73 -0
  91. package/dist/src/layouts/geometric/spiral.js.map +1 -0
  92. package/dist/src/layouts/hierarchical/bfs.d.ts +12 -0
  93. package/dist/src/layouts/hierarchical/bfs.js +62 -0
  94. package/dist/src/layouts/hierarchical/bfs.js.map +1 -0
  95. package/dist/src/layouts/hierarchical/bipartite.d.ts +16 -0
  96. package/dist/src/layouts/hierarchical/bipartite.js +72 -0
  97. package/dist/src/layouts/hierarchical/bipartite.js.map +1 -0
  98. package/dist/src/layouts/hierarchical/index.d.ts +6 -0
  99. package/dist/src/layouts/hierarchical/index.js +7 -0
  100. package/dist/src/layouts/hierarchical/index.js.map +1 -0
  101. package/dist/src/layouts/hierarchical/multipartite.d.ts +12 -0
  102. package/dist/src/layouts/hierarchical/multipartite.js +73 -0
  103. package/dist/src/layouts/hierarchical/multipartite.js.map +1 -0
  104. package/dist/src/layouts/index.d.ts +8 -0
  105. package/dist/src/layouts/index.js +9 -0
  106. package/dist/src/layouts/index.js.map +1 -0
  107. package/dist/src/layouts/specialized/index.d.ts +5 -0
  108. package/dist/src/layouts/specialized/index.js +6 -0
  109. package/dist/src/layouts/specialized/index.js.map +1 -0
  110. package/dist/src/layouts/specialized/planar.d.ts +14 -0
  111. package/dist/src/layouts/specialized/planar.js +47 -0
  112. package/dist/src/layouts/specialized/planar.js.map +1 -0
  113. package/dist/src/layouts/specialized/spectral.d.ts +14 -0
  114. package/dist/src/layouts/specialized/spectral.js +106 -0
  115. package/dist/src/layouts/specialized/spectral.js.map +1 -0
  116. package/dist/src/types/embedding.d.ts +9 -0
  117. package/dist/src/types/embedding.js +5 -0
  118. package/dist/src/types/embedding.js.map +1 -0
  119. package/dist/src/types/graph.d.ts +10 -0
  120. package/dist/src/types/graph.js +5 -0
  121. package/dist/src/types/graph.js.map +1 -0
  122. package/dist/src/types/index.d.ts +6 -0
  123. package/dist/src/types/index.js +7 -0
  124. package/dist/src/types/index.js.map +1 -0
  125. package/dist/src/types/layout.d.ts +6 -0
  126. package/dist/src/types/layout.js +5 -0
  127. package/dist/src/types/layout.js.map +1 -0
  128. package/dist/src/utils/graph.d.ts +34 -0
  129. package/dist/src/utils/graph.js +69 -0
  130. package/dist/src/utils/graph.js.map +1 -0
  131. package/dist/src/utils/index.d.ts +8 -0
  132. package/dist/src/utils/index.js +9 -0
  133. package/dist/src/utils/index.js.map +1 -0
  134. package/dist/src/utils/numpy.d.ts +17 -0
  135. package/dist/src/utils/numpy.js +101 -0
  136. package/dist/src/utils/numpy.js.map +1 -0
  137. package/dist/src/utils/params.d.ts +17 -0
  138. package/dist/src/utils/params.js +22 -0
  139. package/dist/src/utils/params.js.map +1 -0
  140. package/dist/src/utils/random.d.ts +14 -0
  141. package/dist/src/utils/random.js +42 -0
  142. package/dist/src/utils/random.js.map +1 -0
  143. package/dist/src/utils/rescale.d.ts +21 -0
  144. package/dist/src/utils/rescale.js +119 -0
  145. package/dist/src/utils/rescale.js.map +1 -0
  146. package/dist/vitest.config.js +1 -1
  147. package/dist/vitest.config.js.map +1 -1
  148. package/package.json +15 -1
  149. package/.env.example +0 -11
  150. package/.github/workflows/ci.yml +0 -101
  151. package/.releaserc.json +0 -22
  152. package/CHANGELOG.md +0 -45
  153. package/CLAUDE.md +0 -104
  154. package/CONTRIBUTING.md +0 -1
  155. package/DEPLOYMENT.md +0 -59
  156. package/commitlint.config.js +0 -37
  157. package/examples/3d-force-directed.html +0 -611
  158. package/examples/3d-kamada-kawai.html +0 -379
  159. package/examples/3d-layout-comparison.html +0 -448
  160. package/examples/3d-spherical-layout.html +0 -319
  161. package/examples/arf-layout.html +0 -524
  162. package/examples/bfs-layout.html +0 -487
  163. package/examples/bipartite-layout.html +0 -382
  164. package/examples/circular-layout.html +0 -292
  165. package/examples/forceatlas2-layout.html +0 -588
  166. package/examples/index.html +0 -241
  167. package/examples/kamada-kawai-layout.html +0 -425
  168. package/examples/layout-helpers.js +0 -486
  169. package/examples/multipartite-layout.html +0 -410
  170. package/examples/planar-layout.html +0 -388
  171. package/examples/random-layout.html +0 -328
  172. package/examples/shell-layout.html +0 -323
  173. package/examples/spectral-layout.html +0 -335
  174. package/examples/spiral-layout.html +0 -447
  175. package/examples/spring-layout.html +0 -313
  176. package/test/arf-layout.test.ts +0 -443
  177. package/test/bfs-layout.test.ts +0 -427
  178. package/test/bipartite-layout.test.ts +0 -344
  179. package/test/circular-layout.test.ts +0 -442
  180. package/test/forceatlas2-layout.test.ts +0 -405
  181. package/test/fruchterman-reingold-layout.test.ts +0 -477
  182. package/test/graph-generators.test.ts +0 -450
  183. package/test/kamada-kawai-layout.test.ts +0 -623
  184. package/test/multipartite-layout.test.ts +0 -404
  185. package/test/planar-layout.test.ts +0 -266
  186. package/test/random-layout.test.ts +0 -254
  187. package/test/rescale-layout.test.ts +0 -373
  188. package/test/shell-layout.test.ts +0 -347
  189. package/test/spectral-layout.test.ts +0 -378
  190. package/test/spiral-layout.test.ts +0 -338
  191. package/test/spring-layout.test.ts +0 -241
  192. package/test/test-utils.ts +0 -34
  193. package/test/utils-graph.test.ts +0 -155
  194. package/test/utils-index.test.ts +0 -77
  195. package/test/utils-numpy.test.ts +0 -272
  196. package/test/utils-params.test.ts +0 -99
  197. package/test/utils-random.test.ts +0 -229
  198. package/tsconfig.json +0 -16
  199. package/vite.config.js +0 -36
  200. package/vitest.config.ts +0 -30
@@ -0,0 +1,322 @@
1
+ import { getNodesFromGraph } from '../../utils/graph';
2
+ import { _processParams } from '../../utils/params';
3
+ import { rescaleLayout } from '../../utils/rescale';
4
+ import { RandomNumberGenerator } from '../../utils/random';
5
+ /**
6
+ * Position nodes using the ForceAtlas2 force-directed algorithm.
7
+ *
8
+ * @param G - Graph
9
+ * @param pos - Initial positions for nodes
10
+ * @param maxIter - Maximum number of iterations
11
+ * @param jitterTolerance - Controls tolerance for node speed adjustments
12
+ * @param scalingRatio - Scaling of attraction and repulsion forces
13
+ * @param gravity - Attraction to center to prevent disconnected components from drifting
14
+ * @param distributedAction - Distributes attraction force among nodes
15
+ * @param strongGravity - Uses a stronger gravity model
16
+ * @param nodeMass - Dictionary mapping nodes to their masses
17
+ * @param nodeSize - Dictionary mapping nodes to their sizes
18
+ * @param weight - Edge attribute for weight
19
+ * @param dissuadeHubs - Whether to prevent hub nodes from clustering
20
+ * @param linlog - Whether to use logarithmic attraction
21
+ * @param seed - Random seed for initial positions
22
+ * @param dim - Dimension of layout
23
+ * @returns Positions dictionary keyed by node
24
+ */
25
+ export function forceatlas2Layout(G, pos = null, maxIter = 100, jitterTolerance = 1.0, scalingRatio = 2.0, gravity = 1.0, distributedAction = false, strongGravity = false, nodeMass = null, nodeSize = null, weight = null, dissuadeHubs = false, linlog = false, seed = null, dim = 2) {
26
+ const processed = _processParams(G, null, dim);
27
+ const graph = processed.G;
28
+ const nodes = getNodesFromGraph(graph);
29
+ if (nodes.length === 0) {
30
+ return {};
31
+ }
32
+ // Initialize random number generator
33
+ const rng = new RandomNumberGenerator(seed ?? undefined);
34
+ // Initialize positions if not provided
35
+ let posArray;
36
+ if (pos === null) {
37
+ pos = {};
38
+ posArray = new Array(nodes.length);
39
+ for (let i = 0; i < nodes.length; i++) {
40
+ posArray[i] = Array(dim).fill(0).map(() => rng.rand() * 2 - 1);
41
+ pos[nodes[i]] = posArray[i];
42
+ }
43
+ }
44
+ else if (Object.keys(pos).length === nodes.length) {
45
+ // Use provided positions
46
+ posArray = new Array(nodes.length);
47
+ for (let i = 0; i < nodes.length; i++) {
48
+ posArray[i] = [...pos[nodes[i]]];
49
+ }
50
+ }
51
+ else {
52
+ // Some nodes don't have positions, initialize within the range of existing positions
53
+ let minPos = Array(dim).fill(Number.POSITIVE_INFINITY);
54
+ let maxPos = Array(dim).fill(Number.NEGATIVE_INFINITY);
55
+ // Find min and max of existing positions
56
+ for (const node in pos) {
57
+ for (let d = 0; d < dim; d++) {
58
+ minPos[d] = Math.min(minPos[d], pos[node][d]);
59
+ maxPos[d] = Math.max(maxPos[d], pos[node][d]);
60
+ }
61
+ }
62
+ posArray = new Array(nodes.length);
63
+ for (let i = 0; i < nodes.length; i++) {
64
+ const node = nodes[i];
65
+ if (pos[node]) {
66
+ posArray[i] = [...pos[node]];
67
+ }
68
+ else {
69
+ posArray[i] = Array(dim).fill(0).map((_, d) => minPos[d] + rng.rand() * (maxPos[d] - minPos[d]));
70
+ pos[node] = posArray[i];
71
+ }
72
+ }
73
+ }
74
+ // Initialize mass and size arrays
75
+ const mass = new Array(nodes.length).fill(0);
76
+ const size = new Array(nodes.length).fill(0);
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+ // Flag to track whether to adjust for node sizes
78
+ const adjustSizes = nodeSize !== null;
79
+ // Set node masses and sizes
80
+ for (let i = 0; i < nodes.length; i++) {
81
+ const node = nodes[i];
82
+ mass[i] = nodeMass && nodeMass[node] ?
83
+ nodeMass[node] :
84
+ (Array.isArray(graph) ? 1 : getNodeDegree(graph, node) + 1);
85
+ size[i] = nodeSize && nodeSize[node] ? nodeSize[node] : 1;
86
+ }
87
+ // Create adjacency matrix
88
+ const n = nodes.length;
89
+ const A = Array(n).fill(0).map(() => Array(n).fill(0));
90
+ // Populate adjacency matrix with edge weights
91
+ const edges = Array.isArray(graph) ? [] : graph.edges();
92
+ const nodeIndices = {};
93
+ nodes.forEach((node, i) => { nodeIndices[node] = i; });
94
+ for (const [source, target] of edges) {
95
+ const i = nodeIndices[source];
96
+ const j = nodeIndices[target];
97
+ // Use edge weight if provided, otherwise default to 1
98
+ let edgeWeight = 1;
99
+ if (weight && !Array.isArray(graph) && graph.getEdgeData) {
100
+ edgeWeight = graph.getEdgeData(source, target, weight) || 1;
101
+ }
102
+ A[i][j] = edgeWeight;
103
+ A[j][i] = edgeWeight; // For undirected graphs
104
+ }
105
+ // Initialize force arrays
106
+ const gravities = Array(n).fill(0).map(() => Array(dim).fill(0));
107
+ const attraction = Array(n).fill(0).map(() => Array(dim).fill(0));
108
+ const repulsion = Array(n).fill(0).map(() => Array(dim).fill(0));
109
+ // Simulation parameters
110
+ let speed = 1;
111
+ let speedEfficiency = 1;
112
+ let swing = 1;
113
+ let traction = 1;
114
+ // Helper function to estimate factor for force scaling
115
+ function estimateFactor(n, swing, traction, speed, speedEfficiency, jitterTolerance) {
116
+ // Optimal jitter parameters
117
+ const optJitter = 0.05 * Math.sqrt(n);
118
+ const minJitter = Math.sqrt(optJitter);
119
+ const maxJitter = 10;
120
+ const minSpeedEfficiency = 0.05;
121
+ // Estimate jitter based on current state
122
+ const other = Math.min(maxJitter, optJitter * traction / (n * n));
123
+ let jitter = jitterTolerance * Math.max(minJitter, other);
124
+ // Adjust speed efficiency based on swing/traction ratio
125
+ if (swing / traction > 2.0) {
126
+ if (speedEfficiency > minSpeedEfficiency) {
127
+ speedEfficiency *= 0.5;
128
+ }
129
+ jitter = Math.max(jitter, jitterTolerance);
130
+ }
131
+ // Calculate target speed
132
+ let targetSpeed = swing === 0 ?
133
+ Number.POSITIVE_INFINITY :
134
+ jitter * speedEfficiency * traction / swing;
135
+ // Further adjust speed efficiency
136
+ if (swing > jitter * traction) {
137
+ if (speedEfficiency > minSpeedEfficiency) {
138
+ speedEfficiency *= 0.7;
139
+ }
140
+ }
141
+ else if (speed < 1000) {
142
+ speedEfficiency *= 1.3;
143
+ }
144
+ // Limit the speed increase
145
+ const maxRise = 0.5;
146
+ speed = speed + Math.min(targetSpeed - speed, maxRise * speed);
147
+ return [speed, speedEfficiency];
148
+ }
149
+ // Main simulation loop
150
+ for (let iter = 0; iter < maxIter; iter++) {
151
+ // Reset forces for this iteration
152
+ for (let i = 0; i < n; i++) {
153
+ for (let d = 0; d < dim; d++) {
154
+ attraction[i][d] = 0;
155
+ repulsion[i][d] = 0;
156
+ gravities[i][d] = 0;
157
+ }
158
+ }
159
+ // Compute pairwise differences and distances
160
+ const diff = Array(n).fill(0).map(() => Array(n).fill(0).map(() => Array(dim).fill(0)));
161
+ const distance = Array(n).fill(0).map(() => Array(n).fill(0));
162
+ for (let i = 0; i < n; i++) {
163
+ for (let j = 0; j < n; j++) {
164
+ if (i === j)
165
+ continue;
166
+ for (let d = 0; d < dim; d++) {
167
+ diff[i][j][d] = posArray[i][d] - posArray[j][d];
168
+ }
169
+ distance[i][j] = Math.sqrt(diff[i][j].reduce((sum, d) => sum + d * d, 0));
170
+ // Prevent division by zero
171
+ if (distance[i][j] < 0.01)
172
+ distance[i][j] = 0.01;
173
+ }
174
+ }
175
+ // Calculate attraction forces
176
+ if (linlog) {
177
+ // Logarithmic attraction model
178
+ for (let i = 0; i < n; i++) {
179
+ for (let j = 0; j < n; j++) {
180
+ if (i === j || A[i][j] === 0)
181
+ continue;
182
+ const dist = distance[i][j];
183
+ const factor = -Math.log(1 + dist) / dist * A[i][j];
184
+ for (let d = 0; d < dim; d++) {
185
+ const force = factor * diff[i][j][d];
186
+ attraction[i][d] += force;
187
+ }
188
+ }
189
+ }
190
+ }
191
+ else {
192
+ // Linear attraction model
193
+ for (let i = 0; i < n; i++) {
194
+ for (let j = 0; j < n; j++) {
195
+ if (i === j || A[i][j] === 0)
196
+ continue;
197
+ for (let d = 0; d < dim; d++) {
198
+ const force = -diff[i][j][d] * A[i][j];
199
+ attraction[i][d] += force;
200
+ }
201
+ }
202
+ }
203
+ }
204
+ // Apply distributed attraction if enabled
205
+ if (distributedAction) {
206
+ for (let i = 0; i < n; i++) {
207
+ for (let d = 0; d < dim; d++) {
208
+ attraction[i][d] /= mass[i];
209
+ }
210
+ }
211
+ }
212
+ // Calculate repulsion forces
213
+ for (let i = 0; i < n; i++) {
214
+ for (let j = 0; j < n; j++) {
215
+ if (i === j)
216
+ continue;
217
+ let dist = distance[i][j];
218
+ // Adjust distance for node sizes if needed
219
+ if (adjustSizes) {
220
+ dist -= size[i] - size[j];
221
+ dist = Math.max(dist, 0.01); // Prevent negative or zero distances
222
+ }
223
+ const distSquared = dist * dist;
224
+ const massProduct = mass[i] * mass[j];
225
+ const factor = (massProduct / distSquared) * scalingRatio;
226
+ for (let d = 0; d < dim; d++) {
227
+ const direction = diff[i][j][d] / dist;
228
+ repulsion[i][d] += direction * factor;
229
+ }
230
+ }
231
+ }
232
+ // Calculate gravity forces
233
+ // First find the center of mass
234
+ const centerOfMass = Array(dim).fill(0);
235
+ for (let i = 0; i < n; i++) {
236
+ for (let d = 0; d < dim; d++) {
237
+ centerOfMass[d] += posArray[i][d] / n;
238
+ }
239
+ }
240
+ for (let i = 0; i < n; i++) {
241
+ const posCentered = Array(dim);
242
+ for (let d = 0; d < dim; d++) {
243
+ posCentered[d] = posArray[i][d] - centerOfMass[d];
244
+ }
245
+ if (strongGravity) {
246
+ // Strong gravity model
247
+ for (let d = 0; d < dim; d++) {
248
+ gravities[i][d] = -gravity * mass[i] * posCentered[d];
249
+ }
250
+ }
251
+ else {
252
+ // Regular gravity model
253
+ const dist = Math.sqrt(posCentered.reduce((sum, val) => sum + val * val, 0));
254
+ if (dist > 0.01) {
255
+ for (let d = 0; d < dim; d++) {
256
+ const direction = posCentered[d] / dist;
257
+ gravities[i][d] = -gravity * mass[i] * direction;
258
+ }
259
+ }
260
+ }
261
+ }
262
+ // Calculate total forces and update positions
263
+ const update = Array(n).fill(0).map(() => Array(dim).fill(0));
264
+ let totalSwing = 0;
265
+ let totalTraction = 0;
266
+ for (let i = 0; i < n; i++) {
267
+ for (let d = 0; d < dim; d++) {
268
+ update[i][d] = attraction[i][d] + repulsion[i][d] + gravities[i][d];
269
+ }
270
+ // Calculate swing and traction for this node
271
+ const oldPos = [...posArray[i]];
272
+ const newPos = oldPos.map((p, d) => p + update[i][d]);
273
+ const swingVector = oldPos.map((p, d) => p - newPos[d]);
274
+ const tractionVector = oldPos.map((p, d) => p + newPos[d]);
275
+ const swingMagnitude = Math.sqrt(swingVector.reduce((sum, val) => sum + val * val, 0));
276
+ const tractionMagnitude = Math.sqrt(tractionVector.reduce((sum, val) => sum + val * val, 0));
277
+ totalSwing += mass[i] * swingMagnitude;
278
+ totalTraction += 0.5 * mass[i] * tractionMagnitude;
279
+ }
280
+ // Update speed and efficiency
281
+ [speed, speedEfficiency] = estimateFactor(n, totalSwing, totalTraction, speed, speedEfficiency, jitterTolerance);
282
+ // Apply forces to update positions
283
+ let totalMovement = 0;
284
+ for (let i = 0; i < n; i++) {
285
+ let factor;
286
+ if (adjustSizes) {
287
+ // Calculate displacement magnitude
288
+ const df = Math.sqrt(update[i].reduce((sum, val) => sum + val * val, 0));
289
+ const swinging = mass[i] * df;
290
+ // Determine scaling factor with size adjustments
291
+ factor = 0.1 * speed / (1 + Math.sqrt(speed * swinging));
292
+ factor = Math.min(factor * df, 10) / df;
293
+ }
294
+ else {
295
+ // Standard scaling factor
296
+ const swinging = mass[i] * Math.sqrt(update[i].reduce((sum, val) => sum + val * val, 0));
297
+ factor = speed / (1 + Math.sqrt(speed * swinging));
298
+ }
299
+ // Apply factor to update position
300
+ for (let d = 0; d < dim; d++) {
301
+ const movement = update[i][d] * factor;
302
+ posArray[i][d] += movement;
303
+ totalMovement += Math.abs(movement);
304
+ }
305
+ }
306
+ // Check for convergence
307
+ if (totalMovement < 1e-10) {
308
+ break;
309
+ }
310
+ }
311
+ // Create position dictionary
312
+ const positions = {};
313
+ for (let i = 0; i < n; i++) {
314
+ positions[nodes[i]] = posArray[i];
315
+ }
316
+ return rescaleLayout(positions);
317
+ }
318
+ // Helper function to get node degree
319
+ function getNodeDegree(graph, node) {
320
+ return graph.edges().filter((edge) => edge[0] === node || edge[1] === node).length;
321
+ }
322
+ //# sourceMappingURL=forceatlas2.js.map
@@ -0,0 +1 @@
1
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@@ -0,0 +1,19 @@
1
+ /**
2
+ * Fruchterman-Reingold force-directed layout algorithm
3
+ */
4
+ import { Graph, Node, PositionMap } from '../../types';
5
+ /**
6
+ * Position nodes using Fruchterman-Reingold force-directed algorithm.
7
+ *
8
+ * @param {Object} G - Graph or list of nodes
9
+ * @param {number} k - Optimal distance between nodes
10
+ * @param {Object} pos - Initial positions for nodes
11
+ * @param {Array} fixed - Nodes to keep fixed at initial position
12
+ * @param {number} iterations - Maximum number of iterations
13
+ * @param {number} scale - Scale factor for positions
14
+ * @param {Array|null} center - Coordinate pair around which to center the layout
15
+ * @param {number} dim - Dimension of layout
16
+ * @param {number} seed - Random seed for initial positions
17
+ * @returns {Object} Positions dictionary keyed by node
18
+ */
19
+ export declare function fruchtermanReingoldLayout(G: Graph, k?: number | null, pos?: PositionMap | null, fixed?: Node[] | null, iterations?: number, scale?: number, center?: number[] | null, dim?: number, seed?: number | null): PositionMap;
@@ -0,0 +1,131 @@
1
+ /**
2
+ * Fruchterman-Reingold force-directed layout algorithm
3
+ */
4
+ import { _processParams } from '../../utils/params';
5
+ import { getNodesFromGraph, getEdgesFromGraph } from '../../utils/graph';
6
+ import { RandomNumberGenerator } from '../../utils/random';
7
+ import { rescaleLayout } from '../../utils/rescale';
8
+ /**
9
+ * Position nodes using Fruchterman-Reingold force-directed algorithm.
10
+ *
11
+ * @param {Object} G - Graph or list of nodes
12
+ * @param {number} k - Optimal distance between nodes
13
+ * @param {Object} pos - Initial positions for nodes
14
+ * @param {Array} fixed - Nodes to keep fixed at initial position
15
+ * @param {number} iterations - Maximum number of iterations
16
+ * @param {number} scale - Scale factor for positions
17
+ * @param {Array|null} center - Coordinate pair around which to center the layout
18
+ * @param {number} dim - Dimension of layout
19
+ * @param {number} seed - Random seed for initial positions
20
+ * @returns {Object} Positions dictionary keyed by node
21
+ */
22
+ export function fruchtermanReingoldLayout(G, k = null, pos = null, fixed = null, iterations = 50, scale = 1, center = null, dim = 2, seed = null) {
23
+ const processed = _processParams(G, center, dim);
24
+ let graph = processed.G;
25
+ center = processed.center;
26
+ const nodes = getNodesFromGraph(graph);
27
+ const edges = getEdgesFromGraph(graph);
28
+ if (nodes.length === 0) {
29
+ return {};
30
+ }
31
+ if (nodes.length === 1) {
32
+ const singlePos = {};
33
+ singlePos[nodes[0]] = center;
34
+ return singlePos;
35
+ }
36
+ // Set up initial positions
37
+ let positions = {};
38
+ if (pos) {
39
+ // Use provided positions
40
+ for (const node of nodes) {
41
+ if (pos[node]) {
42
+ positions[node] = [...pos[node]];
43
+ }
44
+ else {
45
+ const rng = new RandomNumberGenerator(seed ?? undefined);
46
+ positions[node] = rng.rand(dim);
47
+ }
48
+ }
49
+ }
50
+ else {
51
+ // Random initial positions
52
+ const rng = new RandomNumberGenerator(seed ?? undefined);
53
+ for (const node of nodes) {
54
+ positions[node] = rng.rand(dim);
55
+ }
56
+ }
57
+ // Set up fixed nodes
58
+ const fixedNodes = new Set(fixed || []);
59
+ // Optimal distance between nodes
60
+ if (!k) {
61
+ k = 1.0 / Math.sqrt(nodes.length);
62
+ }
63
+ // Initialize temperature
64
+ let t = 0.1;
65
+ // Calculate temperature reduction
66
+ const dt = t / (iterations + 1);
67
+ // Simple cooling schedule
68
+ for (let i = 0; i < iterations; i++) {
69
+ // Calculate repulsive forces
70
+ const displacement = {};
71
+ for (const node of nodes) {
72
+ displacement[node] = Array(dim).fill(0);
73
+ }
74
+ // Repulsive forces between nodes
75
+ for (let v1i = 0; v1i < nodes.length; v1i++) {
76
+ const v1 = nodes[v1i];
77
+ for (let v2i = v1i + 1; v2i < nodes.length; v2i++) {
78
+ const v2 = nodes[v2i];
79
+ // Difference vector
80
+ const delta = positions[v1].map((p, i) => p - positions[v2][i]);
81
+ // Distance
82
+ const distance = Math.sqrt(delta.reduce((sum, d) => sum + d * d, 0)) || 0.1;
83
+ // Force
84
+ const force = (k * k) / distance;
85
+ // Add force to displacement
86
+ for (let j = 0; j < dim; j++) {
87
+ const direction = delta[j] / distance;
88
+ displacement[v1][j] += direction * force;
89
+ displacement[v2][j] -= direction * force;
90
+ }
91
+ }
92
+ }
93
+ // Attractive forces between connected nodes
94
+ for (const [source, target] of edges) {
95
+ // Difference vector
96
+ const delta = positions[source].map((p, i) => p - positions[target][i]);
97
+ // Distance
98
+ const distance = Math.sqrt(delta.reduce((sum, d) => sum + d * d, 0)) || 0.1;
99
+ // Force
100
+ const force = (distance * distance) / k;
101
+ // Add force to displacement
102
+ for (let j = 0; j < dim; j++) {
103
+ const direction = delta[j] / distance;
104
+ displacement[source][j] -= direction * force;
105
+ displacement[target][j] += direction * force;
106
+ }
107
+ }
108
+ // Update positions
109
+ for (const node of nodes) {
110
+ if (fixedNodes.has(node))
111
+ continue;
112
+ // Calculate displacement magnitude
113
+ const magnitude = Math.sqrt(displacement[node].reduce((sum, d) => sum + d * d, 0));
114
+ // Limit maximum displacement by temperature
115
+ const limitedMagnitude = Math.min(magnitude, t);
116
+ // Update position
117
+ for (let j = 0; j < dim; j++) {
118
+ const direction = magnitude === 0 ? 0 : displacement[node][j] / magnitude;
119
+ positions[node][j] += direction * limitedMagnitude;
120
+ }
121
+ }
122
+ // Cool temperature
123
+ t -= dt;
124
+ }
125
+ // Rescale positions
126
+ if (!fixed) {
127
+ positions = rescaleLayout(positions, scale, center);
128
+ }
129
+ return positions;
130
+ }
131
+ //# sourceMappingURL=fruchterman-reingold.js.map
@@ -0,0 +1 @@
1
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@@ -0,0 +1,8 @@
1
+ /**
2
+ * Force-directed layout algorithms
3
+ */
4
+ export { springLayout } from './spring';
5
+ export { fruchtermanReingoldLayout } from './fruchterman-reingold';
6
+ export { kamadaKawaiLayout } from './kamada-kawai';
7
+ export { forceatlas2Layout } from './forceatlas2';
8
+ export { arfLayout } from './arf';
@@ -0,0 +1,9 @@
1
+ /**
2
+ * Force-directed layout algorithms
3
+ */
4
+ export { springLayout } from './spring';
5
+ export { fruchtermanReingoldLayout } from './fruchterman-reingold';
6
+ export { kamadaKawaiLayout } from './kamada-kawai';
7
+ export { forceatlas2Layout } from './forceatlas2';
8
+ export { arfLayout } from './arf';
9
+ //# sourceMappingURL=index.js.map
@@ -0,0 +1 @@
1
+ {"version":3,"file":"index.js","sourceRoot":"","sources":["../../../../src/layouts/force-directed/index.ts"],"names":[],"mappings":"AAAA;;GAEG;AAEH,OAAO,EAAE,YAAY,EAAE,MAAM,UAAU,CAAC;AACxC,OAAO,EAAE,yBAAyB,EAAE,MAAM,wBAAwB,CAAC;AACnE,OAAO,EAAE,iBAAiB,EAAE,MAAM,gBAAgB,CAAC;AACnD,OAAO,EAAE,iBAAiB,EAAE,MAAM,eAAe,CAAC;AAClD,OAAO,EAAE,SAAS,EAAE,MAAM,OAAO,CAAC"}
@@ -0,0 +1,15 @@
1
+ import type { Graph, PositionMap } from '../../types';
2
+ import type { DistanceMap } from '../../algorithms/optimization';
3
+ /**
4
+ * Position nodes using Kamada-Kawai path-length cost-function.
5
+ *
6
+ * @param G - NetworkX graph or list of nodes
7
+ * @param dist - A two-level dictionary of optimal distances between nodes
8
+ * @param pos - Initial positions for nodes
9
+ * @param weight - The edge attribute used for edge weights
10
+ * @param scale - Scale factor for positions
11
+ * @param center - Coordinate pair around which to center the layout
12
+ * @param dim - Dimension of layout
13
+ * @returns Positions dictionary keyed by node
14
+ */
15
+ export declare function kamadaKawaiLayout(G: Graph, dist?: DistanceMap | null, pos?: PositionMap | null, weight?: string, scale?: number, center?: number[] | null, dim?: number): PositionMap;
@@ -0,0 +1,87 @@
1
+ import { getNodesFromGraph } from '../../utils/graph';
2
+ import { _processParams } from '../../utils/params';
3
+ import { rescaleLayout } from '../../utils/rescale';
4
+ import { circularLayout } from '../geometric/circular';
5
+ import { _computeShortestPathDistances, _kamadaKawaiSolve } from '../../algorithms/optimization';
6
+ /**
7
+ * Position nodes using Kamada-Kawai path-length cost-function.
8
+ *
9
+ * @param G - NetworkX graph or list of nodes
10
+ * @param dist - A two-level dictionary of optimal distances between nodes
11
+ * @param pos - Initial positions for nodes
12
+ * @param weight - The edge attribute used for edge weights
13
+ * @param scale - Scale factor for positions
14
+ * @param center - Coordinate pair around which to center the layout
15
+ * @param dim - Dimension of layout
16
+ * @returns Positions dictionary keyed by node
17
+ */
18
+ export function kamadaKawaiLayout(G, dist = null, pos = null, weight = 'weight', scale = 1, center = null, dim = 2) {
19
+ const processed = _processParams(G, center, dim);
20
+ const graph = processed.G;
21
+ center = processed.center;
22
+ const nodes = getNodesFromGraph(graph);
23
+ if (nodes.length === 0) {
24
+ return {};
25
+ }
26
+ if (nodes.length === 1) {
27
+ return { [nodes[0]]: center };
28
+ }
29
+ // Initialize distance matrix
30
+ if (!dist) {
31
+ // Kamada-Kawai requires a proper Graph, not just a list of nodes
32
+ if (Array.isArray(graph)) {
33
+ throw new Error('Kamada-Kawai layout requires a Graph with edges, not just a list of nodes');
34
+ }
35
+ dist = _computeShortestPathDistances(graph, weight);
36
+ }
37
+ // Convert distances to a matrix
38
+ const nodesArray = Array.from(nodes);
39
+ const nNodes = nodesArray.length;
40
+ const distMatrix = Array(nNodes).fill(0).map(() => Array(nNodes).fill(1e6));
41
+ for (let i = 0; i < nNodes; i++) {
42
+ const nodeI = nodesArray[i];
43
+ distMatrix[i][i] = 0;
44
+ if (!dist[nodeI])
45
+ continue;
46
+ for (let j = 0; j < nNodes; j++) {
47
+ const nodeJ = nodesArray[j];
48
+ if (dist[nodeI][nodeJ] !== undefined) {
49
+ distMatrix[i][j] = dist[nodeI][nodeJ];
50
+ }
51
+ }
52
+ }
53
+ // Initialize positions if not provided
54
+ if (!pos) {
55
+ if (dim >= 2) {
56
+ // Use circular/spherical layout for 2D and 3D
57
+ pos = circularLayout(G, 1, center, dim);
58
+ }
59
+ else {
60
+ // For 1D, use a linear layout
61
+ const posArray = {};
62
+ nodesArray.forEach((node, i) => {
63
+ posArray[node] = [i / (nNodes - 1 || 1)];
64
+ });
65
+ pos = posArray;
66
+ }
67
+ }
68
+ // Convert positions to array for computation
69
+ const posArray = new Array(nNodes);
70
+ for (let i = 0; i < nNodes; i++) {
71
+ const node = nodesArray[i];
72
+ posArray[i] = pos[node] ? [...pos[node]] : Array(dim).fill(0);
73
+ // Ensure correct dimensionality
74
+ while (posArray[i].length < dim) {
75
+ posArray[i].push(0);
76
+ }
77
+ }
78
+ // Run the Kamada-Kawai algorithm
79
+ const newPositions = _kamadaKawaiSolve(distMatrix, posArray, dim);
80
+ // Convert positions array back to dictionary and rescale
81
+ const finalPos = {};
82
+ for (let i = 0; i < nNodes; i++) {
83
+ finalPos[nodesArray[i]] = newPositions[i];
84
+ }
85
+ return rescaleLayout(finalPos, scale, center);
86
+ }
87
+ //# sourceMappingURL=kamada-kawai.js.map
@@ -0,0 +1 @@
1
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