Hi!
I was wondering if it is possible to overlay two drawings of the same graph where I use different color-coded vertex sizes? Theses colors would need to be transparent and the graph layout must match in each drawing. Is there an easy way of doing so with graph-tool?
Thanks!
Regards,
Hi Sebastian,
On 03/28/2011 10:17 AM, Sebastian Weber wrote:
I was wondering if it is possible to overlay two drawings of the same graph where I use different color-coded vertex sizes?
The only way of _actually_ overlaying (without modifying the graph) would be to create two png or svg figures, and overlaying them with some graphics software/library.
If you want to modify the graph, you can draw it first to obtain the positions, then duplicate the vertices and/or edges, copy the positions and set the colors you want, and then you have your "overlay".
Theses colors would need to be transparent and the graph layout must match in each drawing.
Transparent colors are no problem, as well as matching the layout (you just need to pass the 'pos' parameter, and set 'pin=True' so that the positions remain fixed).
Cheers, Tiago
Hi,
I am quite new to graph-tool and mostly use it for drawing at the moment. Thanks Tiago for all the great work you put into graph-tool!
Apologies for hijacking this thread - I hope this okay as my question is basically the same that Sebastian had.
Tiago Peixoto wrote:
Theses colors would need to be transparent and the graph layout must match in each drawing.
Transparent colors are no problem, as well as matching the layout (you just need to pass the 'pos' parameter, and set 'pin=True' so that the positions remain fixed).
That's exactly what I tried, but for me, every time I call gt.graph_draw, I get a new layout.
Here's my code:
#create network and properties... #first plot. this works fine positions = gt.graph_draw(network, vcolor=colorProperties, vcmap=colorMap, vnorm=False, vorder=plotOrder, output='out0.png')
# change a few values in colorProperties and plotOrder
# now draw again gt.graph_draw(network,pos=positions,pin=True,vcolor=colorProperties,vcmap=colorMap,vnorm=False,output='out1.png')
-- However, what happens is that the graph gets a new layout which is distinct from the first one. Is there something I missed? I also tried to add vprops={'pin':'True} to the second call of graph_draw, but that didn't help either.
I'm on Ubuntu 11.04, graph-tool version 2.2.14 (commit 39b848dc, Sat Jul 9 00:53:56 2011 +0200) [from ppa], graphviz version 2.26.3.
Cheers, Steffen
-- 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.
This might not be very helping, but I gave up back then, when I had the problem. A solution would be great though…
Cheers
Am 08.08.2011 um 16:20 schrieb Steffen Schaper:
Hi,
I am quite new to graph-tool and mostly use it for drawing at the moment. Thanks Tiago for all the great work you put into graph-tool!
Apologies for hijacking this thread - I hope this okay as my question is basically the same that Sebastian had.
Tiago Peixoto wrote:
Theses colors would need to be transparent and the graph layout must match in each drawing.
Transparent colors are no problem, as well as matching the layout (you just need to pass the 'pos' parameter, and set 'pin=True' so that the positions remain fixed).
That's exactly what I tried, but for me, every time I call gt.graph_draw, I get a new layout.
Here's my code:
#create network and properties... #first plot. this works fine positions = gt.graph_draw(network, vcolor=colorProperties, vcmap=colorMap, vnorm=False, vorder=plotOrder, output='out0.png')
# change a few values in colorProperties and plotOrder
# now draw again gt.graph_draw(network,pos=positions,pin=True,vcolor=colorProperties,vcmap=colorMap,vnorm=False,output='out1.png')
-- However, what happens is that the graph gets a new layout which is distinct from the first one. Is there something I missed? I also tried to add vprops={'pin':'True} to the second call of graph_draw, but that didn't help either.
I'm on Ubuntu 11.04, graph-tool version 2.2.14 (commit 39b848dc, Sat Jul 9 00:53:56 2011 +0200) [from ppa], graphviz version 2.26.3.
Cheers, Steffen
-- 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. _______________________________________________ graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
I think I found a way forward - may not be perfect, but works for the time being.
It looks like pin only works with neato and fdp - see http://www.graphviz.org/doc/info/attrs.html#d:pin
So I added layout='neato' to graph_draw, and that seems to do the trick. Unfortunately, the canvas size seems to change (even though I specified size=(15,15) for the initial layout and for the later call). My current workaround is to simply redraw the graph with neato and overwrite the output file.
One thing that suprised me is that pinning doesn't make things any faster. My network has almost 10000 nodes - does it really take most of the time to create output rather than performing the actual layout?
Cheers, Steffen
On 08/08/11 16:28, Sebastian Weber wrote:
This might not be very helping, but I gave up back then, when I had the problem. A solution would be great though…
Cheers
Am 08.08.2011 um 16:20 schrieb Steffen Schaper:
Hi,
I am quite new to graph-tool and mostly use it for drawing at the moment. Thanks Tiago for all the great work you put into graph-tool!
Apologies for hijacking this thread - I hope this okay as my question is basically the same that Sebastian had.
Tiago Peixoto wrote:
Theses colors would need to be transparent and the graph layout must match in each drawing.
Transparent colors are no problem, as well as matching the layout (you just need to pass the 'pos' parameter, and set 'pin=True' so that the positions remain fixed).
That's exactly what I tried, but for me, every time I call gt.graph_draw, I get a new layout.
Here's my code:
#create network and properties... #first plot. this works fine positions = gt.graph_draw(network, vcolor=colorProperties, vcmap=colorMap, vnorm=False, vorder=plotOrder, output='out0.png')
# change a few values in colorProperties and plotOrder
# now draw again gt.graph_draw(network,pos=positions,pin=True,vcolor=colorProperties,vcmap=colorMap,vnorm=False,output='out1.png')
-- However, what happens is that the graph gets a new layout which is distinct from the first one. Is there something I missed? I also tried to add vprops={'pin':'True} to the second call of graph_draw, but that didn't help either.
I'm on Ubuntu 11.04, graph-tool version 2.2.14 (commit 39b848dc, Sat Jul 9 00:53:56 2011 +0200) [from ppa], graphviz version 2.26.3.
Cheers, Steffen
-- 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. _______________________________________________ graph-tool mailing list graph-tool@skewed.de http://lists.skewed.de/mailman/listinfo/graph-tool
On 08/08/2011 04:20 PM, Steffen Schaper wrote:
However, what happens is that the graph gets a new layout which is distinct from the first one. Is there something I missed? I also tried to add vprops={'pin':'True} to the second call of graph_draw, but that didn't help either.
Strange, I cannot reproduce this at all... For me, I get always the same layout.
What version of graphviz do you have insalled?
Cheers, Tiago
On 08/08/2011 05:03 PM, Steffen Schaper wrote:
I think I found a way forward - may not be perfect, but works for the time being.
It looks like pin only works with neato and fdp - see http://www.graphviz.org/doc/info/attrs.html#d:pin
So I added layout='neato' to graph_draw, and that seems to do the trick.
The graph_draw() function defaults to 'neato' if the graph is smaller than 1000 nodes, and uses 'sfdp' otherwise. And indeed, it seems like 'sfdp' ignores the pin property. This is a graphviz limitation.
Unfortunately, the canvas size seems to change (even though I specified size=(15,15) for the initial layout and for the later call). My current workaround is to simply redraw the graph with neato and overwrite the output file.
Unfortunately, graphviz gives very little control on the total canvas size, and likes to crop things. I find it very annoying, but I don't know how to force graphviz to do the right thing.
One thing that suprised me is that pinning doesn't make things any faster. My network has almost 10000 nodes - does it really take most of the time to create output rather than performing the actual layout?
I notice a _huge_ difference when running 'neato' with pinning vs. without. But maybe you can improve things further by limiting the total number of iterations with the 'maxiter' parameter.
Cheers, Tiago
On 09/08/11 01:34, Tiago de Paula Peixoto wrote:
Strange, I cannot reproduce this at all... For me, I get always the same layout.
What version of graphviz do you have insalled?
I'm on version 2.26.3 (20100126.1600) - the one in the Ubuntu Natty repos.
On 09/08/11 01:48, Tiago de Paula Peixoto wrote:
The graph_draw() function defaults to 'neato' if the graph is smaller than 1000 nodes, and uses 'sfdp' otherwise. And indeed, it seems like 'sfdp' ignores the pin property. This is a graphviz limitation.
Maybe you could add another check to draw/__init__.py at line 312:
layout = "neato" if g.num_vertices() <= 1000 else "fdp" if pos is not None and pin else "sfdp"
Unfortunately, graphviz gives very little control on the total canvas size, and likes to crop things. I find it very annoying, but I don't know how to force graphviz to do the right thing.
At least when I set the canvas size for neato with size=(15,15), I always get the same size in the end.
One thing that suprised me is that pinning doesn't make things any faster. My network has almost 10000 nodes - does it really take most of the time to create output rather than performing the actual layout?
I notice a _huge_ difference when running 'neato' with pinning vs. without. But maybe you can improve things further by limiting the total number of iterations with the 'maxiter' parameter.
Thanks, setting maxiter=1 made things faster (subjectively, I haven't done timings). What I meant originally was that the difference between sfdp without pin and neato/fdp (I tried both now) with pin isn't as big as I thought. My naive expectation was that it takes most of the time to do the layout, so if we tell graphviz where to put the nodes, the rest should be a lot quicker.
Best, Steffen
On 08/09/2011 10:48 AM, Steffen Schaper wrote:
The graph_draw() function defaults to 'neato' if the graph is smaller than 1000 nodes, and uses 'sfdp' otherwise. And indeed, it seems like 'sfdp' ignores the pin property. This is a graphviz limitation.
Maybe you could add another check to draw/__init__.py at line 312:
layout = "neato" if g.num_vertices() <= 1000 else "fdp" if pos is not None and pin else "sfdp"
Yes, something like this would be a good idea.
Thanks, setting maxiter=1 made things faster (subjectively, I haven't done timings). What I meant originally was that the difference between sfdp without pin and neato/fdp (I tried both now) with pin isn't as big as I thought. My naive expectation was that it takes most of the time to do the layout, so if we tell graphviz where to put the nodes, the rest should be a lot quicker.
Although the difference between sfdp and fdp/neato is very noticeable for larger graphs, I would expect that both fdp/neato with pin=True would be _much_ faster than sfdp, since the layout algorithm is not run. In my experience, this is always what I found. I would be interested in understanding why you perceive this not to be the case... How long does it actually take to plot with sfdp and neato with pinning?
Cheers, Tiago
On 11/08/11 08:52, Tiago de Paula Peixoto wrote:
Although the difference between sfdp and fdp/neato is very noticeable for larger graphs, I would expect that both fdp/neato with pin=True would be _much_ faster than sfdp, since the layout algorithm is not run. In my experience, this is always what I found. I would be interested in understanding why you perceive this not to be the case... How long does it actually take to plot with sfdp and neato with pinning?
I've just done a few timings using layout='neato' (or layout='fdp'),pos=positions,pin=True,maxiter=0. This takes about 11 seconds for my network. I had used maxiter=1 earlier, and that made neato a lot slower (more than a factor of 2) while fdp's performance didn't change much. sfdp takes about 15 seconds. In all cases, I specified vcolor, vcmap and vorder. So you're completely right: neato/fdp are a lot faster given the layout and the right arguments.
I also experimented with matplotlib - given that I got the positions out of graph-tool/graphviz, the rest can also be done there. The speed is a little better there - it takes just under 10 seconds. Also, I want to do many plots with the same layout (just different vertex colours), so I think matplotlib is more convenient for me. I can plot the network once and afterwards only draw the vertices whose colour changes, and then use imagemagick/composite to do the overlay.
Cheers, Steffen
-
Sebastian Weber -
Steffen Schaper -
Tiago de Paula Peixoto