I was wondering if someone could help with the following problem.
I have a dozen nodes, each a different sized circle between 0 - 10. I have a distance for each node-pair (e.g. node A and B are 6 from each other, etc.)
Given this data, would it be possible to compute the position of each node on a grid?
The distance could be from the centre or the edge of a node.
Thanks.
If you just want to have a graph to look at, try building a neato file where you specify edge distance. Neato is a layout program that is part of the GraphViz package.
This is quite easy. Your example above would look like this:
graph G {
A -- B [len=6]
}
Related
I've been trying to find a way to replicate the following network graph format in R using DiagrammeR/GraphViz, but without success (ignore the thick black arrow on N1): https://i.stack.imgur.com/oHpQz.png
The graph is a directed graph and each edge in a certain direction either ends with an arrowhead (-->) if the edge value is positive, or a circle/odot (--o) if the edge value is negative. Between a pair of nodes (ex. N1 -- A1), there can be an edge N1 --> A1 and an edge A1 --o N1, and these need to be concentrated so that the two edges look like one line with an arrowhead on one end and a circlehead on the opposite end (like this: o--->). These cannot be parallel or look like two edges ideally.
Another requirement is that the nodes have to be in very specific positions and remain there throughout model simulations where edges might change. From what I have tried and the documentation I have read, this is not possible to do in DOT format, but is possible in neato format.
This is where I get a problem. In neato, I can align the nodes exactly where I want them by defining their x,y positions. However, when I use concentrate = true to create the o---> edge from two otherwise parallel edges, only one type of arrowhead remains. So an edge that's supposed to look like o---> ends up looking like ---> or o---.
This is not a problem in DOT format as concentrate = true does what I want it to do, but in DOT I cannot assign exact node positions. I have tried getting around this using node ranks but without much luck. It seems to stack nodes I want in different ranks within the same rank. As well, concentrate = true doesn't seem to work for edges between nodes within the same rank, as it leaves them as two separate curved edges ---> and o--- without concentrating them.
The reason why I need this to work is because I'm running model simulations where the edges change, and I need to generate hundreds of such graphs. For easy comparison, the nodes need to stay in the same place for consistency.
This is the closest I could come up with using neato format (nodes are positioned the way I want but it's not showing the proper o---> for all the black edges minus self-edges; red edges are true one-way links): https://i.stack.imgur.com/YJBY7.jpg
If only the edges showed up as the proper o---> format, this would be perfect for my needs. If you know of any way to fix this issue using DiagrammeR/GraphViz, or even another program, I would be so grateful. Thanks!
You probably don't need concentrate. Look at arrowtail and dir (https://www.graphviz.org/doc/info/attrs.html#d:arrowtail and https://www.graphviz.org/doc/info/attrs.html#d:dir) and neato -n
digraph c {
graph[label="can neato do the work?"]
node[shape=circle]
a [pos="100,100"]
b [pos="200,100"]
c [pos="300,100"]
a->b [dir=both arrowtail=odot]
c->c [dir=both arrowtail=odot arrowhead=none]
}
Giving:
I am making a game in Unity3d and I need a pathfinding algorithm that can guide enemy's towards the player on a 3d surface. The problem is that the 3d surface can take any shape, so it can be a 3d sphere, cube, torus and many more shapes.
I tried using A* but for that formula I need the distance between the two points, and since the object is curved I cannot get that so easily. I found that you can use the Haversine formula if its a sphere, but that won't work on a torus or a random 3d shape.
I want this kind of result except with every kind of object:
https://www.youtube.com/watch?v=hvunNq7yVcU
Is there a way/algorithm that I can use to get that result. I know there is something called nav mesh but I need to program it myself. Also I cannot find how nav mesh approaches this dilema. I am going to use the triangles of my object as nodes.
So my question boils down to:
Does anyone know a algorithm for pathfinding that works on any 3d surface?
Thanks in advance.
I think your problem is that you are not using a graph, I would suggest that you look into a tutorial on how to create a graph, for the language you are using if you can, (this may also help here they are using edges to connect their node which is needed if you have more then one weight). If you do make a graph you will need a node class. Each node must contain pointers to any nodes that it is connected to and an ID of some kind. In your case that is probably all you need but it is also possible to assign a weight to each move if you also have an edge class (connectors between nodes) which would be used to connect the nodes. If you do have an edge class your nodes will have pointers to edges instead of other nodes and each edge will have a weight and a pointer to 1 or 2 nodes (depending on if it is a directed path or not). You can also make a graph class to contain all of your nodes and edges.
Summary:
make a node class and determine if you need the edge class (if everything has a weight of 1 you can get away with out it). Use the node class to create a graph to represent your map with each tile being a node with pointers to connected tiles. Use A* or dijkstra's algorithm to search your graph to find the shortest path.
note: most examples you will find will be for 2d graphs, yours is no different except that there are no bounds on yours, you just need to connect the nodes to their adjacent tiles.
Given two points (vertices), say i and j represented by small circles. How can I draw an arc (arrow) connecting those two vertices in Javafx 8? Surprisingly, very little information exists on drawing arcs in javafx8.
Given two points,(vertices), say i and j and a number of arcs between the two vertices. For each arc a direction is given. So for example, I can have 2 arcs from i to j, and 1 arc from j to i. How can I draw these arcs in javafx 8 such that they don't overlap each other. I was thinking on drawing each arc as half of an oval.
Normally I would provide sample code, but here I really have no clue how to draw an arc in between two points in Javafx?
Here is an example of something I would like to draw:
In my application I know the exact coordinates for the vertices a,b,c,d. I just need to know how to draw the arcs (I would favor a faster, simple solution over a pretty solution).
I have started to work with gephi to help me display a dataset.
The dataset contains:
tags (terms for a certain picture) as nodes
Normalized Google Similarity Distance between those tags as edges with a weight (between 0 und 1)
Every tag is connected to every other tag, as long as they both belong to the same picture. So I have one cluster of nodes and edges for every picture.
I have now imported this dataset to gephi in the following format:
nodes: id, label
edges: target, source, weight (between 0 and 1)
Like 500 nodes and 6000 edges.
My problem now is that after importing all those nodes and edges the graph looks kind of bunched with no real order. Every cluster of every picture is mixed into other clusters of other pictures.
Now using Modularity as Partition algorithm (which should use the Louvain method) the graph is getting colored, each color represent a picture. Now I can split this mess, using the Force Atlas 2 Layout.
I now have a colored graph with something like 15 clusters (every cluster represent 1 picture)
Now I want to cluster those clusters again using tags (nodes) according to their Normalized google distance (weight of the edges), which should then be tags which are somewhat equal in their meaning.
I hope you guys understand what I want to accomplish.
I can also upload a picture to clarify it.
Thanks a lot
I don't think you can do that with the standard version of Gephi. You would need to develop a plugin to implement the very last step of your process.
Gephi is good for visualizing and browsing graphs, but (for now) there are more complete tools when it comes to processing topological properties. for instance, the igraph library (available in C, R and python) might be more appropriate for you. And note that you can use a file format compatible with both Gephi and igraph, which allows you to use both tools on the same data.
I was able to solve my problem. I had to import every one of these 15 clusters on their own. In this way i could use the Modularity method on just those few.
I need to visualize a relatively large graph (6K nodes, 8K edges) that has the following properties:
Distinct Clusters. Approximately 50-100 Nodes per cluster and moderate interconnectivity at the cluster level
Minimal (5-10 inter-cluster edges per cluster) interconnectivity between clusters
Let global edge overlap = The edge overlaps caused by directly visualizing a graph of Clusters = {A, B, C, D, E}, Edges = {Pentagram of those clusters, which is non-planar by the way and will definitely generate edge overlap if you draw it out directly}
Let Local Edge Overlap = the above but { A, B, C, D, E } are just nodes.
I need to visualize graphs with the above in a way that satisfies the following requirements
No global edge overlap (i.e. edge overlaps caused by inter-cluster properties is not okay)
Local edge overlap within a cluster is fine
Anyone have thoughts on how to best visualize a graph with the requirements above?
One solution I've come up with to deal with the global edge overlap is to make sure a cluster A can only have a max of 1 direct edge to another cluster (B) during visualization. Any additional inter-cluster edges between cluster A -> C, A -> D, ... are disconnected and additional node/edges A -> A_C, C -> C_A, A -> A_D, D -> D_A... are created.
Anyone have any thoughts?
Prefuse has some good graph drawing link text algorithms built in and it seems to handle fairly large graphs relatively well. You might try Flow Map Layout which is built on top of Prefuse.
Given your objectives, I think that the Fruchterman-Reingold algorithm does a pretty decent job of preventing edge overlap. See for example this screenshot of a network consisting of multiple components drawn using the Fruchterman-Reingold algorithm. IGraph has built-in support for this algorithm (as does Networkx I believe) and is really fast.
There is a program built on top of Prefuse called SocialAction. You have to request the code from the author, but it does a lot of statistical analysis on the graph for you, such as identifying subgraphs. I've used it on a graph with more than 18,000 nodes, and although it is very slow at that scale it still works.
Although it may be silly to ask at this point, had you tried out http://www.graphviz.org/ ?
I haven't seen too many graph visualization tools that support separating clusters within a graph visually. One option might be to take a look at WilmaScope. It looks to have some support for cluster based layouts.
Organic layout manages fairly well clustered graphs in yFiles framework. Try first in yEd to see if it does what needed. It is probably reasonable to use nested graphs alias groups for each cluster. Organic layout has feature called Group Layout Policy which can be used if layout needs to be done using different principles for inter-cluster and intra-cluster edges, with incremental layouting. With some effort, one can translate graph into GraphML to avoid manual work.