vis.js node placement when physics is disabled - vis.js

How can you disable physics in vis.js with a large number of nodes and no edges without having all the nodes appear in a circle? Pastebin is disabled for work, so I won't post everything, but here are my options:
var options = {
physics: { enabled: false },
layout: { improvedLayout: false }
}
For some reason all the nodes appear in a circle. When I reenable physics, they are correctly spaced out. I would appreciate any help anyone could give me.

I'm the developer of the network module of vis.js. What you're seeing is the default starting position. The improved layout is a solution to this which you also disable.. What exactly are you expecting to get out of this? The physics position the nodes. Without it they are randomly positioned.
You can manually provide x and y values to nodes, you can try hierarchical or if you want to turn physics off AFTER they are positioned, use the stabilizationIterationsDone event.
These events are shown in our examples and documentation.
Good luck!

Related

visIgraphLayout causing display issues for shiny app

I can share the code if needed but it felt like a lot to share to start, so I'll try to explain narratively. I am creating an interface to display network data (as you might have guessed from the title). My first issue has been going on for a few days where visIgraphLayout is not laying out my visual correctly. Regardless of using "full" or "square" as the "type", the network map extends beyond the edge of the display space. When I resize the interface window, then the map will snap to full. Why won't it simply resize automatically? If it matters, I do have the output space in a box element. Also, I have the layout styles working off radiobuttons, and when I switch between styles the map goes beyond the edges again.
Part 2 begins. While the above problem is annoying, it was livable. However, a new wrinkle popped up. I added some font size control to my visNodes code - i.e., radiobuttons set to switch between off (0), small (5), standard (14), and large (40) font size options. Once I implemented this code, when I resize the interface window, now the network map disappears completely after initial load. If I select a new label option, it will redraw but beyond the edges of the space.
All the issues resolve themselves if I ditch the visIgraphLayout, but then I lose the layout functionality which I really like.
I hope this is clear enough. I really appreciate any insights the community might provide. Be well.
I think I have figured out an answer. Long story short, certain pieces didn't work and play well with others. Went through and build it again, and all it good.
Cheers.

Cystoscape - node and spoke model - need bounciness and movement

I have a visualization of node and spoke model and tried cytoscape. Loving how easy it is to implement and able to control the size of the node, color of the node, placement of text etc. On load, the viz eases out and appears. Sort of like https://ivis-at-bilkent.github.io/cytoscape.js-fcose/demo.html.
However once it is loaded, it looks very static.
I do not want to go to d3 / amcharts just for this reason. Is there anyway I can float nodes around or something using cytoscape options or even css like codepen.io/team/amcharts/pen/EJgNey
Use Cola. Refer to the demo: https://js.cytoscape.org/demos/colajs-graph/
Cola can be used iteratively, as in the demo with the slider: The slider restarts the layout with the updated state -- here the slider controls the forces. You can just restart the layout whenever a node is dragged.

Layout Nodes - Space Between Nodes?

I'm visualizing a network with VisJS, and using the default layout with physics enabled. When nodes are added, a layout is done and the nodes are placed on the canvas. However, some of my nodes are quite large. Is there a way to force the amount of space that is left between nodes?
I've tried setting the size of the node, which doesn't seem to have an effect. The shape of the node is "square".
Figured this out, I was missing physics options for the engine I was using, in particular "avoidOverlap".

Mermaid change position of nodes / options Anyway to fix nodes' position

I'm trying to draw a flow chart in html.
The flow must be configured as below.
I've tried it in Mermaid like this
<script src="https://cdnjs.cloudflare.com/ajax/libs/mermaid/9.0.1/mermaid.min.js"></script>
<div class="mermaid">
graph LR
A-->B
B-->C
C-->B
C-->D
D-->C
D-->E
E-->D
E-->F
F-->E
F-->G
G-->E
C-->E
H
A-->H
H-->E;
</div>
Please I want to fix the position from A to G horizontality
I've tried to use CSS position, never worked.
Also tried to animate it through jquery, never worked.
Please let me know any way to fix these nodes or else great library for it.
Thanks.
I get what you mean, but after having a look to the documentation, I could not manage to get your result, only improve readability by adding linkStyle default interpolate basis at the beginning of the chart.
It is unfortunate not to be able to put the nodes in separate divs, that could do the trick with some align. You are not the only one asking for similar behaviour in the repository of mermaid.
The API doc of the mermaid flowcharts does not provide any setting to achieve your goal.
Although the difficulty seems to come from the fact mermaid-js is based on d3-shape to make the links between nodes as stated here.
My best advice is to change library and since you are coding in javascript, vis.js can get you the result you expect with the networks as you can see here.
I did not dig any further, but it seems you may have to define manually the coordinates of the nodes, as explained in this stackoverflow post : vis.js - Place node manually

ScalaFX: How to couple 2 figures rotationally in perspective

A basic rotating question - How you can couple 2 figures (a box/cube with a sphere in it ANYWHERE in the cube, BUT in the center) so that these 2 are coupled ROTATIONALLY (that is why I don't want the sphere to be in the center of the cube) IN PERSPECTIVE.
In other words, when I rotate the cube with the mouse and "bring" the sphere closer to the front (say, make a 180-degree rotation), the perspective changes accordingly and the sphere gets bigger visually (compared to the position on the back)?
Asked a couple of ScalaFX experts - they both said it was a very good question and recommended to post it here.
Cheers:
Zar
>
I'm not entirely sure what you're trying to do, but you can can rotate multiple objects by applying a Rotate transform to the Group that contains all of those objects. If you only want to rotate some of the objects, but not all of them, you have to structure the scene so that the objects being rotated have a common parent Group - with none of the non-rotating objects belonging to it. Applying Rotate transforms to that parent Group will rotate all of its child objects too. Rotation will be about the origin of that parent Group.
Update: I forgot to mention how to address the issue of perspective. The 3D objects in a scene aren't directly affected by perspective, since perspective is a property of how the scene is rendered. This rendering is performed by Camera objects. To render the scene using perspective (as opposed to using orthogonal, or parallel, as it's referred to in JavaFX/ScalaFX), add a PerspectiveCamera to the scene and view the scene using that camera. For further information on this, refer to the following: Getting Started with JavaFX 3D Graphics: Camera
Update 2: I've created a gist on GitHub with a complete program for doing this.
Update 3: Made box transparent & moved sphere inside the box. Now left/primary mouse button rotates box + sphere when dragged; right/secondary mouse button moves camera dolly towards/away from boxes, changing perspective accordingly.
Update 4: So, if I understand you right, you want to transform the shapes in your 3D scene so that they look as though perspective has been applied to them. Do I have that right?
If so, the reason that this is not a "built-in" capability is for the reasons outlined below. Please forgive me if you already know all of this, incidentally - I'm just trying to provide a comprehensive answer. :-)
Scene graphs (as typically used by retained mode 3D systems, such as JavaFX) capture the geometry, location, rotation, color, etc. of a 3D scene in a hierarchical tree structure. The idea is that the modeler only need to worry about the content of the scene - ensuring dimensions, alignments, etc. are correct - and do not need to worry about how the scene is rendered.
Perspective can be applied when the scene is rendered as it would appear from a specific viewpoint; i.e. when the scene is translated into a 2D projection such as a GUI window. (The process of determining what the scene looks like in perspective is a part of the rendering algorithm - but does not require modification, deformation, etc. of the scene.) If perspective is not enabled, then the scene is typically rendered orthogonally, without any vanishing points, apparent scaling, etc. The key point here is that the scene itself is unaffected by how it is viewed.
With this arrangement, it's possible to have multiple views of the same scene. Not only can they each have a different viewpoint, but some can be orthogonal and some can use perspective - yet each can render the scene correctly without any confusing artifacts. If it worked the way you seem to think it does, then you could only ever have a single view of the scene at a time, as the scene would need to be deformed during rendering to look right from that sole viewpoint. When editing the scene, you'd need to remove those deformations to prevent mind-blowing confusion for the modeler.
In short, it's a very unusual requirement that the scene itself be deformed to show what it would look like in perspective. That's why there's no built-in capability to do this in any 3D system that I know of.
Assuming that you wish to proceed - using JavaFX - here's some points to bear in mind:
I don't believe that the regular 3D primitives (namely Box, Sphere & Cylinder) can be deformed to represent a perspective view of them. You will have to construct the shapes using the TriangleMesh and MeshView objects (the former captures the geometry of the shape, the latter allows it to be treated as a 3D shape).
To apply perspective, you would have to reposition the vertices in the TriangleMesh instances to deform the scene appropriately. If you need to be able to change the viewpoint, or rotate the box & sphere, then these changes would need to be dynamic, so that the calculated vertex coordinates react to the changing viewpoint and/or rotation. Because of fish-eye effects at high levels of perspective dilation, you might need more vertices than you might expect.
Given your requirements, you still need a camera to view the scene. Clearly, you cannot use the PerspectiveCamera to render the scene, or it will treat the scene as unadjusted and will apply a second level of perspective, ruining your carefully calculated deformations. You will then need to use ParallelCamera to produce orthogonal views of your scene.
Unfortunately, JavaFX's support for using ParallelCamera with 3D scenes is still very immature. (The ParallelCamera is primarily used to render 2D scenes, such as dialogs, buttons, menu's, sliders, etc.) You might find it difficult to use in practice. (You can approximate an orthogonal projection using the PerspectiveCamera by utilizing a very narrow field of view and moving the camera away from the scene by some distance. You would also need to adjust the clipping planes to avoid the image disappearing.)
Finally, at some point, you will need to be able to position the camera at the same location as the viewpoint being used for the perspective deformation. When the camera is synchronized with that viewpoint, then your scene - although rendered orthogonally - will appear as a correct perspective projection of the intended scene. Whenever the camera and the viewpoint are separated, the scene will appear unnatural and distorted, which - I understand - is your intention.
In summary, I would say that what you intend to do is far from trivial, and the implementation is way beyond the scope of a StackOverflow answer. Good luck!
Mike:
Sorry for the delay, I am finishing something for a client in a totally different application area and pulled-away from my "teaching perspective" toy ...
Just got the notification for the new answers and had a quick look - one thing I noticed right away was that the sphere is outside rather than inside the transparent box (haven’t looked at the code yet).
What I actually expected was a "built-in" perspective "argument" (either in the rotation transformation, or the scene definition, or a stand-alone function - in one way are another), which allows for different perspective to be rendered depending on the angle between the 2 (initially) parallel opposing edges at the bottom, for example. I understand of course that in reality it depends on the ViewPoint Position and you are not "allowed" to forcefully change this angle, but the goal here is simply a "cause-and-effect" toy in a 3D scene.
Controlling the camera will not allow for that, since it imposes the perspective very smoothly (as it would be in real life) rather than allowing the child to directly control the edges and immediately see how her action changes the perspective, rather than playing with the viewpoint.
As mentioned in the original question, I'd expect a function like the one sketched below (and I would expect it to be BUILT-IN in a sensible 3D-product since it is so basic, rather than forcing me or you to manually craft some code for something that should have been there from the get-go - perspective is simply a basic fundamental and hopefully will be covered by the rendering in some form in the next release):
def doPersepctive( myBox: MyBoxContainer, angle: Int, viewPoint: Point): Int = {
// Presents the perspective look in a way defined by the "angle" between the
// (initially) parallel edges of myBoxContainer, from the viewPoint Point (3D).
// Rotate everything within the boundaries of MyBoxContainer. The
// bigger the angle, the smaller the sphere at the back, of course.
// Returns the rotatedAngle after the mouseEvent to enable auto-replay later, so
// the kid can examine what her actions were and see the effect of those actions.
}
Tnx again for your entry, I will certainly have a look at the code, and reply - but you see the general picture above. Sorry for the delay again:
Z
>
Mike:
This is more like the original intension - although I find merits in the first attempt too, actually.
I made the sphere (in the first version) transparent (via diffuseColor = Color.web("#ffff0080") ), so now she can play with both versions, and both are pretty much SIMILAR from a child's perspective (meaning one of the objects is transparent, moreover different objects in these versions).
Now - I tried to make the BOX transparent (where the sphere is outside) and I failed - is there a reason for that? In other words trying to make the object passing "behind" visible? One transparent object passing behind another transparent object, so to say?
In the second version I ALSO cannot see "behind the object", meaning I can NOT see the EDGE of the box passing behind the sphere. Not only that – I can NOT see the back edge EVEN when it is not behind the sphere (but only behind the front side of the box)!
My question in a sense is "CAN both objects be made transparent" - I guess this is the closest to what I am trying to ask. May be with different “transparency %”, but still transparent…
Tnx again:
Zar
>
Yes, Mike - your answer was completely relevant and I do accept it with the thoughtfully-explained shortcomings of the current ScalaFX implementation. If I need to "click" somewhere to formally TAG this, please let me know - I am new to this group and don't know the formalities really.
Tnx again:
Zar
I expected that there was a parameter that controls the Perspective during a Rotational Transformation, but cannot find one. The sample problem is clearly defined - you have a BOX/CUBE and a smaller sphere inside; now when you rotate the BOX, the sphere rotates WITH it but "in perspective", meaning that if you bring the sphere in front, it looks (draws) bigger correspondingly with the "perspective".
Zar
>
>
BTW, if it were possible to add the Sphere as a child of the Box, then you ...
<
That is not possible, but CAN I add the sphere AT RUN TIME rather than at compile time? In other words is there an "addObject" that adds the sphere after the kid has played with box for 1 min and 1 min after running the program, the sphere appears. Cannot see anything like that here:
http://www.scalafx.org/api/8.0/index.html#package
May be I am missing something ?
Zar
>

Resources