图形中的弹性（动画）边，节点对邻居施加引力？
Elastic (animated) edges in graph with nodes exerting gravitational pull on neighbours?
是否有 Cytoscape 的布局扩展，可以实现类似于 Neo4j 浏览器的动态行为，即当您拖动节点时，它的边缘在某种程度上是弹性的，但是 也会沿途拖动连接的节点 （我称之为局部重力）？
更新：
我正在处理的示例使用 CoSE Bilkent (compound) layout extension, but it doesn't seem to support the effect/animation I'm after out of the box. I had hoped the scarcely documented { gravity: 1 } option might be related - after all, when a node pulls other nodes along, that could well be described as gravity - but changing the setting on a small sample graph had no such effect; some digging ensued and I now think that setting has to do with how close to the graph's center nodes are displayed. I then looked at all layout demos, none seem to display the effect I'm after out of the box. AllegroViva appears to implement similar behavior (video)，但据我了解，它在该视频中呈现时间序列（因此可能只是手动重绘图形）。他们的网站好像也挂了。
我正在寻找的是简单的、开箱即用的，或者可以快速实施的。不幸的是，我不太确定 什么是我想要的正确搜索词（尤其是在 Cytoscape 的域中）。因此我问什么是公认的非常高层次的问题。今天，我发现 Visjs 称它为 physics events (or at least uses the effect I'm after as part of that demo) - but as I mentioned, gravity in Cytoscape is apparently not what I'm looking for. At this point, however, I'm merely trying to establish if Cytoscape is the right library, or whether I need to look at others, like Alchemy (cf. its Philosophers' Relatedness example)。
答案：
感谢您编辑问题，我想我可以帮助您解决这个问题。 Cytoscape.js 有这个功能深埋在 extension layouts, specifically in cytoscape.js-cola. The layout is a physics layout with "springy" like nodes, so that the distance between them stays the same. The catch here is, that in the paragraph Notes 中，作者这样描述：
- If you want to maintain interactivity, you probably should not mix infinite: true with fit: true. Fitting naturally changes the zoom level, making dragging misaligned and feel weird to users --- though it still works technically. Better to just fit: false when infinite: true, and cy.center() or cy.fit() on layoutready.
- The alignment option isn't as flexible as the raw Cola option. Here, only integers can be used to specify relative positioning, so it's a bit limited. If you'd like to see a more sophisticated implementation, please send a pull request.
代码：
所以这个例子应该可行（请注意节点可以移动，但由于它们已经处于最佳位置，它们往往会保持编队）：
document.addEventListener("DOMContentLoaded", function() {
var cy = (window.cy = cytoscape({
container: document.getElementById("cy"),
autounselectify: true,
boxSelectionEnabled: false,
layout: {
name: "cola",
infinite: true,
fit: false
},
style: [{
selector: "node",
css: {
"background-color": "#f92411"
}
},
{
selector: "edge",
css: {
"line-color": "#f92411"
}
}
],
elements: {
nodes: [{
data: {
id: "1",
label: "P"
}
},
{
data: {
id: "2",
label: "sucrose phosphate phosphatase"
}
},
{
data: {
id: "4",
label: "sucrose 6-phosphate"
}
},
{
data: {
id: "6",
label: "sucrose"
}
},
{
data: {
id: "8",
label: "invertase"
}
},
{
data: {
id: "10",
label: "fructose"
}
},
{
data: {
id: "12",
label: "fructokinase"
}
},
{
data: {
id: "14",
label: "fructose 6-phosphate"
}
},
{
data: {
id: "20",
label: "phosphoglucose isomerase"
}
},
{
data: {
id: "22",
label: "glucose 6-phosphate"
}
},
{
data: {
id: "28",
label: "glucose"
}
},
{
data: {
id: "30",
label: "hexokinase"
}
},
{
data: {
id: "33",
label: "sucrose synthase"
}
},
{
data: {
id: "36",
label: "UDP - glucose"
}
},
{
data: {
id: "38",
label: "sucrose phosphate synthase"
}
},
{
data: {
id: "41",
label: "UDP"
}
},
{
data: {
id: "44",
label: "fructose 6-phosphate"
}
},
{
data: {
id: "46",
label: "ATP"
}
},
{
data: {
id: "47",
label: "ATP"
}
},
{
data: {
id: "52",
label: "ATP"
}
},
{
data: {
id: "57",
label: "ADP"
}
},
{
data: {
id: "66",
label: "PP"
}
},
{
data: {
id: "71",
label: "UTP"
}
},
{
data: {
id: "76",
label: "UDP glucose pyrophosphorylase"
}
},
{
data: {
id: "80",
label: "glucose 1-phosphate"
}
},
{
data: {
id: "86",
label: "phospho- glucomutase (cPGM)"
}
},
{
data: {
id: "89",
label: "G1P transporter"
}
},
{
data: {
id: "90",
label: "P"
}
},
{
data: {
id: "95",
label: "P"
}
},
{
data: {
id: "102",
label: "P"
}
},
{
data: {
id: "103",
label: "P"
}
},
{
data: {
id: "104",
label: "G6P transporter"
}
},
{
data: {
id: "109",
label: "glucose 6-phosphate"
}
},
{
data: {
id: "115",
label: "phospho- glucomutase (cPGM)"
}
},
{
data: {
id: "121",
label: "glucose 1-phosphate"
}
},
{
data: {
id: "128",
label: "ADPglucose pyrophosphorylase (pAGPase)"
}
},
{
data: {
id: "130",
label: "ADP - glucose"
}
},
{
data: {
id: "136",
label: "PP"
}
},
{
data: {
id: "141",
label: "ATP"
}
},
{
data: {
id: "148",
label: "inorganic diphosphatase"
}
},
{
data: {
id: "149",
label: "P"
}
},
{
data: {
id: "156",
label: "phosphate transporter"
}
},
{
data: {
id: "158",
label: "P"
}
},
{
data: {
id: "164",
label: "starch synthase (simpl.)"
}
},
{
data: {
id: "166",
label: "ADP"
}
},
{
data: {
id: "172",
label: "starch"
}
},
{
data: {
id: "178",
label: "ATP/ADP transporter"
}
},
{
data: {
id: "179",
label: "ADP"
}
},
{
data: {
id: "184",
label: "ADP"
}
},
{
data: {
id: "189",
label: "ATP"
}
}
],
edges: [{
data: {
source: "2",
target: "1"
}
},
{
data: {
source: "4",
target: "2"
}
},
{
data: {
source: "2",
target: "6"
}
},
{
data: {
source: "6",
target: "8"
}
},
{
data: {
source: "8",
target: "10"
}
},
{
data: {
source: "12",
target: "14"
}
},
{
data: {
source: "14",
target: "20"
}
},
{
data: {
source: "20",
target: "22"
}
},
{
data: {
source: "8",
target: "28"
}
},
{
data: {
source: "28",
target: "30"
}
},
{
data: {
source: "30",
target: "22"
}
},
{
data: {
source: "6",
target: "33"
}
},
{
data: {
source: "33",
target: "10"
}
},
{
data: {
source: "33",
target: "36"
}
},
{
data: {
source: "36",
target: "38"
}
},
{
data: {
source: "38",
target: "4"
}
},
{
data: {
source: "38",
target: "41"
}
},
{
data: {
source: "41",
target: "33"
}
},
{
data: {
source: "44",
target: "38"
}
},
{
data: {
source: "52",
target: "12"
}
},
{
data: {
source: "12",
target: "57"
}
},
{
data: {
source: "46",
target: "30"
}
},
{
data: {
source: "30",
target: "47"
}
},
{
data: {
source: "71",
target: "76"
}
},
{
data: {
source: "76",
target: "66"
}
},
{
data: {
source: "76",
target: "36"
}
},
{
data: {
source: "80",
target: "76"
}
},
{
data: {
source: "22",
target: "86"
}
},
{
data: {
source: "86",
target: "80"
}
},
{
data: {
source: "95",
target: "89"
}
},
{
data: {
source: "89",
target: "90"
}
},
{
data: {
source: "102",
target: "104"
}
},
{
data: {
source: "80",
target: "89"
}
},
{
data: {
source: "104",
target: "109"
}
},
{
data: {
source: "115",
target: "109"
}
},
{
data: {
source: "121",
target: "89"
}
},
{
data: {
source: "121",
target: "115"
}
},
{
data: {
source: "121",
target: "128"
}
},
{
data: {
source: "128",
target: "130"
}
},
{
data: {
source: "141",
target: "128"
}
},
{
data: {
source: "128",
target: "136"
}
},
{
data: {
source: "136",
target: "148"
}
},
{
data: {
source: "148",
target: "149"
}
},
{
data: {
source: "149",
target: "156"
}
},
{
data: {
source: "156",
target: "158"
}
},
{
data: {
source: "130",
target: "164"
}
},
{
data: {
source: "164",
target: "166"
}
},
{
data: {
source: "178",
target: "179"
}
},
{
data: {
source: "184",
target: "178"
}
},
{
data: {
source: "178",
target: "189"
}
},
{
data: {
source: "141",
target: "178"
}
},
{
data: {
source: "104",
target: "103"
}
},
{
data: {
source: "10",
target: "12"
}
},
{
data: {
source: "164",
target: "172"
}
},
{
data: {
source: "22",
target: "104"
}
}
]
}
}));
cy.unbind("tapend");
cy.bind("tapend", "node", function() {
cy.animate({
fit: {
eles: cy.elements(),
padding: 20
},
center: {
eles: cy.elements()
}
}, {
duration: 500
});
});
});
body {
font-family: helvetica;
font-size: 14px;
}
#cy {
width: 100%;
height: 100%;
position: absolute;
left: 0;
top: 0;
z-index: 999;
}
h1 {
opacity: 0.5;
font-size: 1em;
}
<!DOCTYPE>
<html>
<head>
<title>cytoscape-cola.js demo</title>
<meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
<script src="https://unpkg.com/cytoscape/dist/cytoscape.min.js"></script>
<!-- for testing with local version of cytoscape.js -->
<!--<script src="../cytoscape.js/build/cytoscape.js"></script>-->
<script src="https://unpkg.com/webcola/WebCola/cola.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/cytoscape-cola@2.3.0/cytoscape-cola.min.js"></script>
</head>
<body>
<h1>cytoscape-cola demo</h1>
<div id="cy"></div>
</body>
</html>
结论：
Cytoscape.js有显示力布局的能力，但比你提供的两个例子差一点（他们可以在不将节点移动到最佳位置的情况下显示图形，但用户更喜欢一个).如果你喜欢使用 cytoscape.js，你可以很好地做到这一点，但始终考虑你需要哪些用例并检查是否有任何其他应用程序可以更好地处理这种情况（cytoscape.js 有很多很棒的功能你可以使用，所以如果你能让它工作，cytoscape 将是我的选择）。
祝你好运！
您可以使用 force-directed layout of d3.js Here is an example graph.
我相信 Neo4j 浏览器也使用 d3.js
来自官网：
The default Neo4j Server has a powerful, customizable data visualization tool based on the built-in D3.js library.
我找到了一个可能与您的问题相似的视频Use of Cytoscape.js for Client project, also there is another extension LAYOUT with d3.js cytoscape.js-d3-force可能是一个很好的参考。
是否有 Cytoscape 的布局扩展，可以实现类似于 Neo4j 浏览器的动态行为，即当您拖动节点时，它的边缘在某种程度上是弹性的，但是 也会沿途拖动连接的节点 （我称之为局部重力）？
更新：
我正在处理的示例使用 CoSE Bilkent (compound) layout extension, but it doesn't seem to support the effect/animation I'm after out of the box. I had hoped the scarcely documented { gravity: 1 } option might be related - after all, when a node pulls other nodes along, that could well be described as gravity - but changing the setting on a small sample graph had no such effect; some digging ensued and I now think that setting has to do with how close to the graph's center nodes are displayed. I then looked at all layout demos, none seem to display the effect I'm after out of the box. AllegroViva appears to implement similar behavior (video)，但据我了解，它在该视频中呈现时间序列（因此可能只是手动重绘图形）。他们的网站好像也挂了。
我正在寻找的是简单的、开箱即用的，或者可以快速实施的。不幸的是，我不太确定 什么是我想要的正确搜索词（尤其是在 Cytoscape 的域中）。因此我问什么是公认的非常高层次的问题。今天，我发现 Visjs 称它为 physics events (or at least uses the effect I'm after as part of that demo) - but as I mentioned, gravity in Cytoscape is apparently not what I'm looking for. At this point, however, I'm merely trying to establish if Cytoscape is the right library, or whether I need to look at others, like Alchemy (cf. its Philosophers' Relatedness example)。
答案：
感谢您编辑问题，我想我可以帮助您解决这个问题。 Cytoscape.js 有这个功能深埋在 extension layouts, specifically in cytoscape.js-cola. The layout is a physics layout with "springy" like nodes, so that the distance between them stays the same. The catch here is, that in the paragraph Notes 中，作者这样描述：
- If you want to maintain interactivity, you probably should not mix infinite: true with fit: true. Fitting naturally changes the zoom level, making dragging misaligned and feel weird to users --- though it still works technically. Better to just fit: false when infinite: true, and cy.center() or cy.fit() on layoutready.
- The alignment option isn't as flexible as the raw Cola option. Here, only integers can be used to specify relative positioning, so it's a bit limited. If you'd like to see a more sophisticated implementation, please send a pull request.
代码：
所以这个例子应该可行（请注意节点可以移动，但由于它们已经处于最佳位置，它们往往会保持编队）：
document.addEventListener("DOMContentLoaded", function() {
var cy = (window.cy = cytoscape({
container: document.getElementById("cy"),
autounselectify: true,
boxSelectionEnabled: false,
layout: {
name: "cola",
infinite: true,
fit: false
},
style: [{
selector: "node",
css: {
"background-color": "#f92411"
}
},
{
selector: "edge",
css: {
"line-color": "#f92411"
}
}
],
elements: {
nodes: [{
data: {
id: "1",
label: "P"
}
},
{
data: {
id: "2",
label: "sucrose phosphate phosphatase"
}
},
{
data: {
id: "4",
label: "sucrose 6-phosphate"
}
},
{
data: {
id: "6",
label: "sucrose"
}
},
{
data: {
id: "8",
label: "invertase"
}
},
{
data: {
id: "10",
label: "fructose"
}
},
{
data: {
id: "12",
label: "fructokinase"
}
},
{
data: {
id: "14",
label: "fructose 6-phosphate"
}
},
{
data: {
id: "20",
label: "phosphoglucose isomerase"
}
},
{
data: {
id: "22",
label: "glucose 6-phosphate"
}
},
{
data: {
id: "28",
label: "glucose"
}
},
{
data: {
id: "30",
label: "hexokinase"
}
},
{
data: {
id: "33",
label: "sucrose synthase"
}
},
{
data: {
id: "36",
label: "UDP - glucose"
}
},
{
data: {
id: "38",
label: "sucrose phosphate synthase"
}
},
{
data: {
id: "41",
label: "UDP"
}
},
{
data: {
id: "44",
label: "fructose 6-phosphate"
}
},
{
data: {
id: "46",
label: "ATP"
}
},
{
data: {
id: "47",
label: "ATP"
}
},
{
data: {
id: "52",
label: "ATP"
}
},
{
data: {
id: "57",
label: "ADP"
}
},
{
data: {
id: "66",
label: "PP"
}
},
{
data: {
id: "71",
label: "UTP"
}
},
{
data: {
id: "76",
label: "UDP glucose pyrophosphorylase"
}
},
{
data: {
id: "80",
label: "glucose 1-phosphate"
}
},
{
data: {
id: "86",
label: "phospho- glucomutase (cPGM)"
}
},
{
data: {
id: "89",
label: "G1P transporter"
}
},
{
data: {
id: "90",
label: "P"
}
},
{
data: {
id: "95",
label: "P"
}
},
{
data: {
id: "102",
label: "P"
}
},
{
data: {
id: "103",
label: "P"
}
},
{
data: {
id: "104",
label: "G6P transporter"
}
},
{
data: {
id: "109",
label: "glucose 6-phosphate"
}
},
{
data: {
id: "115",
label: "phospho- glucomutase (cPGM)"
}
},
{
data: {
id: "121",
label: "glucose 1-phosphate"
}
},
{
data: {
id: "128",
label: "ADPglucose pyrophosphorylase (pAGPase)"
}
},
{
data: {
id: "130",
label: "ADP - glucose"
}
},
{
data: {
id: "136",
label: "PP"
}
},
{
data: {
id: "141",
label: "ATP"
}
},
{
data: {
id: "148",
label: "inorganic diphosphatase"
}
},
{
data: {
id: "149",
label: "P"
}
},
{
data: {
id: "156",
label: "phosphate transporter"
}
},
{
data: {
id: "158",
label: "P"
}
},
{
data: {
id: "164",
label: "starch synthase (simpl.)"
}
},
{
data: {
id: "166",
label: "ADP"
}
},
{
data: {
id: "172",
label: "starch"
}
},
{
data: {
id: "178",
label: "ATP/ADP transporter"
}
},
{
data: {
id: "179",
label: "ADP"
}
},
{
data: {
id: "184",
label: "ADP"
}
},
{
data: {
id: "189",
label: "ATP"
}
}
],
edges: [{
data: {
source: "2",
target: "1"
}
},
{
data: {
source: "4",
target: "2"
}
},
{
data: {
source: "2",
target: "6"
}
},
{
data: {
source: "6",
target: "8"
}
},
{
data: {
source: "8",
target: "10"
}
},
{
data: {
source: "12",
target: "14"
}
},
{
data: {
source: "14",
target: "20"
}
},
{
data: {
source: "20",
target: "22"
}
},
{
data: {
source: "8",
target: "28"
}
},
{
data: {
source: "28",
target: "30"
}
},
{
data: {
source: "30",
target: "22"
}
},
{
data: {
source: "6",
target: "33"
}
},
{
data: {
source: "33",
target: "10"
}
},
{
data: {
source: "33",
target: "36"
}
},
{
data: {
source: "36",
target: "38"
}
},
{
data: {
source: "38",
target: "4"
}
},
{
data: {
source: "38",
target: "41"
}
},
{
data: {
source: "41",
target: "33"
}
},
{
data: {
source: "44",
target: "38"
}
},
{
data: {
source: "52",
target: "12"
}
},
{
data: {
source: "12",
target: "57"
}
},
{
data: {
source: "46",
target: "30"
}
},
{
data: {
source: "30",
target: "47"
}
},
{
data: {
source: "71",
target: "76"
}
},
{
data: {
source: "76",
target: "66"
}
},
{
data: {
source: "76",
target: "36"
}
},
{
data: {
source: "80",
target: "76"
}
},
{
data: {
source: "22",
target: "86"
}
},
{
data: {
source: "86",
target: "80"
}
},
{
data: {
source: "95",
target: "89"
}
},
{
data: {
source: "89",
target: "90"
}
},
{
data: {
source: "102",
target: "104"
}
},
{
data: {
source: "80",
target: "89"
}
},
{
data: {
source: "104",
target: "109"
}
},
{
data: {
source: "115",
target: "109"
}
},
{
data: {
source: "121",
target: "89"
}
},
{
data: {
source: "121",
target: "115"
}
},
{
data: {
source: "121",
target: "128"
}
},
{
data: {
source: "128",
target: "130"
}
},
{
data: {
source: "141",
target: "128"
}
},
{
data: {
source: "128",
target: "136"
}
},
{
data: {
source: "136",
target: "148"
}
},
{
data: {
source: "148",
target: "149"
}
},
{
data: {
source: "149",
target: "156"
}
},
{
data: {
source: "156",
target: "158"
}
},
{
data: {
source: "130",
target: "164"
}
},
{
data: {
source: "164",
target: "166"
}
},
{
data: {
source: "178",
target: "179"
}
},
{
data: {
source: "184",
target: "178"
}
},
{
data: {
source: "178",
target: "189"
}
},
{
data: {
source: "141",
target: "178"
}
},
{
data: {
source: "104",
target: "103"
}
},
{
data: {
source: "10",
target: "12"
}
},
{
data: {
source: "164",
target: "172"
}
},
{
data: {
source: "22",
target: "104"
}
}
]
}
}));
cy.unbind("tapend");
cy.bind("tapend", "node", function() {
cy.animate({
fit: {
eles: cy.elements(),
padding: 20
},
center: {
eles: cy.elements()
}
}, {
duration: 500
});
});
});
body {
font-family: helvetica;
font-size: 14px;
}
#cy {
width: 100%;
height: 100%;
position: absolute;
left: 0;
top: 0;
z-index: 999;
}
h1 {
opacity: 0.5;
font-size: 1em;
}
<!DOCTYPE>
<html>
<head>
<title>cytoscape-cola.js demo</title>
<meta name="viewport" content="width=device-width, user-scalable=no, initial-scale=1, maximum-scale=1">
<script src="https://unpkg.com/cytoscape/dist/cytoscape.min.js"></script>
<!-- for testing with local version of cytoscape.js -->
<!--<script src="../cytoscape.js/build/cytoscape.js"></script>-->
<script src="https://unpkg.com/webcola/WebCola/cola.min.js"></script>
<script src="https://cdn.jsdelivr.net/npm/cytoscape-cola@2.3.0/cytoscape-cola.min.js"></script>
</head>
<body>
<h1>cytoscape-cola demo</h1>
<div id="cy"></div>
</body>
</html>
结论：
Cytoscape.js有显示力布局的能力，但比你提供的两个例子差一点（他们可以在不将节点移动到最佳位置的情况下显示图形，但用户更喜欢一个).如果你喜欢使用 cytoscape.js，你可以很好地做到这一点，但始终考虑你需要哪些用例并检查是否有任何其他应用程序可以更好地处理这种情况（cytoscape.js 有很多很棒的功能你可以使用，所以如果你能让它工作，cytoscape 将是我的选择）。
祝你好运！
您可以使用 force-directed layout of d3.js Here is an example graph.
我相信 Neo4j 浏览器也使用 d3.js
来自官网：
The default Neo4j Server has a powerful, customizable data visualization tool based on the built-in D3.js library.
我找到了一个可能与您的问题相似的视频Use of Cytoscape.js for Client project, also there is another extension LAYOUT with d3.js cytoscape.js-d3-force可能是一个很好的参考。