I haven't yet begun to use graph-tool, but it seems like a very good option for analysis of large graphs. I'll be using it to analyze graphs with 50-100,000 nodes, often densely connected (adjacency matrices are about 70% sparse). What I would like to know is how graph-tool will work for visualizing such graphs. I have tried a couple of stand-alone visualization programs with poor results. I would also like to have the option to embed the graph in three dimensions according to spatial coordinates that I specify. How will graph-tool suite my needs? If it's not optimal, can someone suggest a visualization tool that can be integrated with graph-tool without too much headache? Thanks in advance. -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 05/01/2014 02:05 PM, codejon wrote:
I haven't yet begun to use graph-tool, but it seems like a very good option for analysis of large graphs. I'll be using it to analyze graphs with 50-100,000 nodes, often densely connected (adjacency matrices are about 70% sparse).
What I would like to know is how graph-tool will work for visualizing such graphs. I have tried a couple of stand-alone visualization programs with poor results. I would also like to have the option to embed the graph in three dimensions according to spatial coordinates that I specify. How will graph-tool suite my needs? If it's not optimal, can someone suggest a visualization tool that can be integrated with graph-tool without too much headache? Thanks in advance.
In general the visualization of very large graphs is always very tricky, unless it has some very strong large-scale structure. In particular spring-block layouts will just give you blobs in that case. I think the best chance you have of getting something useful is by visualizing it in hierarchy form, such as this: https://graph-tool.skewed.de/static/doc/draw.html#graph_tool.draw.get_hierar... Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
Thanks for your reply Tiago. I do appreciate that I won't be able to see much structure in my graph using something like a spring layout, and a hierarchical layout would be better for exposing interesting features of the graph structure. However I would also like to have the ability to assign three dimensional (x,y,z) node coordinates to each node. This is because each node in my graph corresponds to a measure position in the brain. Surprisingly it's been hard to find graph visualization software that allows the user to specify node positions programmatically for large graphs. Does graph-tool allow the user to do this? -- View this message in context: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/... Sent from the Main discussion list for the graph-tool project mailing list archive at Nabble.com.
On 05/09/2014 07:25 PM, codejon wrote:
Thanks for your reply Tiago. I do appreciate that I won't be able to see much structure in my graph using something like a spring layout, and a hierarchical layout would be better for exposing interesting features of the graph structure. However I would also like to have the ability to assign three dimensional (x,y,z) node coordinates to each node. This is because each node in my graph corresponds to a measure position in the brain. Surprisingly it's been hard to find graph visualization software that allows the user to specify node positions programmatically for large graphs. Does graph-tool allow the user to do this?
Graph-tool does not have any 3D visualization routines. But what do you mean with specifying the node positions 'programmatically'? In graph tool you can pass any position property map to the graph_draw() function... Best, Tiago -- Tiago de Paula Peixoto <tiago@skewed.de>
By programmatically I just mean passing coordinates to a function like graph-draw. But does graph_draw() accept z coordinates, or only (x,y) coordinates? I assume it is only (x,y) since you say that graph-tool does not have 3D visualization. I suppose I could write code to project a 3d set of nodes onto a 2d plane, and then alter node sizes to add the effect of perspective. But I am hoping to find a program that does this natively and quickly for large graphs. Thanks again! On Sat, May 10, 2014 at 7:07 AM, Tiago Peixoto [via Main discussion list for the graph-tool project] <ml-node+s982480n4025514h1@n3.nabble.com> wrote:
On 05/09/2014 07:25 PM, codejon wrote:
Thanks for your reply Tiago. I do appreciate that I won't be able to see much structure in my graph using something like a spring layout, and a hierarchical layout would be better for exposing interesting features of the graph structure. However I would also like to have the ability to assign three dimensional (x,y,z) node coordinates to each node. This is because each node in my graph corresponds to a measure position in the brain. Surprisingly it's been hard to find graph visualization software that allows the user to specify node positions programmatically for large graphs. Does graph-tool allow the user to do this?
Graph-tool does not have any 3D visualization routines.
But what do you mean with specifying the node positions 'programmatically'? In graph tool you can pass any position property map to the graph_draw() function...
Best, Tiago
-- Tiago de Paula Peixoto <[hidden email]<http://user/SendEmail.jtp?type=node&node=4025514&i=0>>
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