Using Wolfram Mathematica 10.0 I'm trying to highlight a subgraph from the whole graph. As can see at the figure, I succeeded to highlight the subgraph and color the nodes and the edges in a specific color (green).
I want that the subgraph will be on the top, such that it will be convenient to see the subgraph edges and nodes.
Anyone know how to do that?
If you used HighlightGraph, you can reorder the vertices of the graph to define the rendering order. Do it manually, or use IGReorderVertices from the IGraph/M package.
Alternatively, check the "Rendering Order" section of the GraphLayout documentation page—it shows how to define the rendering order without changing the order of the vertex list.
Apparently can do that in an easy way, using "Show":
Show[original graph, subgraph].
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 trying to draw a graph using Graphviz in Dot language, and this graph has edges which runs through nodes.
Please see the attached picture below.
So far I did not able to find a way to do this. Any help would be highly appreciated!.
Thanks in advance. ( Tips on any other way to render a graph like this would also be really helpful )
The information above is not that sufficient, however you can check the Drawing with Constrained ranks (Ref: Drawing graphs with dot by "Emden Gansner and Eleftherios Koutsofios and Stephen North").
Graph with constrained ranks
Please read the below for more information :Drawing graphs with dot
Had the same issue today, this worked for me in layout=dot.
(1) setting splines to false
(2) have the specific edge attribute constraint set to false, for edges which must go through another node.
splines=false
x -> y [constraint=false]
Be aware it only worked OK because I did not use a label for the edge.
Using the edge attributes taillabel and headlabel worked for me.
I know that for coloring graph nodes, backtracking/brute force is a common solution. But I was wondering if using DFS I can also achieve a solution ?
Backtracking gives you the opportunity to go back and try other color possibility in order to paint all the nodes with N colors
DFS will start from one node and color it, then jump to its neighbor and color it in different color than its neighbors etc ...
I did a search about using this method but I didn't find an algorithm that uses this.
Question: Is using DFS possible for coloring graph nodes. If yes, is it more efficient than backtracking ?
Thank you
I believe there is some confusion when comparing backtracking and DFS wrt vertex coloring. DFS traversal for a graph gives full enumeration of its vertices in a sequence related to its structure. It does not, however, constitute a full enumeration for the vertex coloring problem, which would require taking into account the possible colors of the vertices.
Thus, if I understand correctly, what you have implemented is a greedy heuristic coloring for a graph directed by DFS.
On the other hand, a backtracking/brute force solution as you name it (such as [Randall-Brown 72]) will provide an exact solution for the minimum coloring problem since it considers every possible vertex coloring. Note that DFS traversal could be used to sort the vertices initially (topological sort) and feed that order to the exact solver.
Using iGraph, how can I represent self-reflexive nodes with circle shaped curves? By default, these curves are represented by a pinched or tear drop shaped loop.
As Spacedman said, you would need to do quite some programming to do this. You could plot a graph without self-loops and then add them (graphs are basically a scatterplot and you can use points and similar functions to add lines to them), but this is not trivial (especially since you need to know the edge of nodes, not their center) and will cause the selfloops to be plotted on top of everything else which might not look good.
This weekend I have updated qgraph with how self-loops work. qgraph can be used to plot networks and should play nicely with igraph. e.g.:
# An adjacency matrix:
A <- matrix(1,3,3)
library("igraph")
# igraph graph and layout:
Graph <- graph.adjacency(A)
Layout <- layout.circle(Graph)
# Plot in qgraph:
library("qgraph")
qgraph(get.adjacency(Graph,sparse=FALSE),layout=Layout,diag=TRUE,directed=TRUE)
I am quite content with how these self-loops turned out and they seem to be more to what you describe. So this could be an option. However, my loops are just as hardcoded. For reference, I compute the edge of a node (starting and ending point of the loop) with the inner function qgraph:::Cent2Edge and compute the shape of the loop (spline) with the inner function qgraph:::SelfLoop.
Inside plot.igraph you can see that loops are drawn using a plot.bezier function, and all the control for that is pretty much hard coded there. You'd have to rewrite large chunks of plot.igraph to call a plot.circle function you'd have to write to do this.
Also, I'm guessing you don't want complete circles, but circle segments that start on the edge of the vertex symbol (the default blue circle with the vertex number in it) and end (possibly with an arrowhead) on another part of the edge of the vertex symbol? Or do you want circles that touch the symbol like the bezier teardrop loops do?
Either way, the answer seems to be 'no, not without doing some programming or submitting a feature request to the igraph guys'
I posted an earlier answer saying the layout functions were involved, but that's not true - the layout functions only position the vertices, and it is plot.igraph's job to draw the edges.
I'm trying to create a graph using Graphviz (complied with neato), and I would like to place nodes in specific locations. For this, I'm specifying exact edge lengths for all edges. However, I don't want all edges to be visible in the final image.
Do you know of any way to hide edges? I should mention that I tried coloring the edges white, but what happens is that I get white lines painted over the graph nodes - it's not very aesthetic...
It can be done using
nodeA -> nodeB [style=invis]
I found out that another way to go is to define:
outputorder="edgesfirst"
for the graph.