graph-tool June 2014

graph-tool@skewed.de

11 participants
26 discussions

HTML label problem
by Johan Mazel 17 Jun '14

17 Jun '14

Hi I want to use some dot files generated for graphviz but I have some parsing issues. I am using HTML labels and it seems to cause problems. Here is my example: graph G { "1" [label=<foo<br/>bar>,shape=box, ]; "2" [shape=box, ]; "1" -- "2" [fontcolor="#FF0000", color="#FF0000", label="2.4e-04", ]; } This HTML label ("label=<foo<br/>bar>") causes this error: Traceback (most recent call last): File "community_graph_tool.py", line 47, in <module> main(sys.argv[1:]) File "community_graph_tool.py", line 30, in main g = load_graph(idotfile) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1956, in load_graph g.load(file_name, fmt, ignore_vp, ignore_ep, ignore_gp) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1712, in load ignore_ep, ignore_gp) RuntimeError: Wanted right bracket to end attribute list (token is "<identifier> 'bar'") If I remove <br/>, I get another error: Traceback (most recent call last): File "community_graph_tool.py", line 47, in <module> main(sys.argv[1:]) File "community_graph_tool.py", line 30, in main g = load_graph(idotfile) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1956, in load_graph g.load(file_name, fmt, ignore_vp, ignore_ep, ignore_gp) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1712, in load ignore_ep, ignore_gp) RuntimeError: Unclosed HTML string (at end of input) And if I completely remove the "label=<foo<br/>bar>,", it also removes all errors. Thanks for your work and time. Johan

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Plotting the clustering coefficient and degree distribution
by Shubham Bhushan 16 Jun '14

16 Jun '14

Hi I tried to get the local clustering coefficient for all the vertices and it returned a property map. I'll be glad if you could tell me how to import data from it and plot it SHubham -- http://about.me/shubham.bhushan

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Re: [graph-tool] graph-tool Digest, Vol 77, Issue 6
by Shubham Bhushan 10 Jun '14

10 Jun '14

Just DFS? Isn't that slow? Maybe Tarjan's? Or Newman-Ziff's? On Tue, Jun 10, 2014 at 5:30 PM, <graph-tool-request(a)skewed.de> wrote: > Send graph-tool mailing list submissions to > graph-tool(a)skewed.de > > To subscribe or unsubscribe via the World Wide Web, visit > http://lists.skewed.de/mailman/listinfo/graph-tool > or, via email, send a message with subject or body 'help' to > graph-tool-request(a)skewed.de > > You can reach the person managing the list at > graph-tool-owner(a)skewed.de > > When replying, please edit your Subject line so it is more specific > than "Re: Contents of graph-tool digest..." > > > Today's Topics: > > 1. Algorithm to find the largest connected cluster (Shubham Bhushan) > 2. Re: Algorithm to find the largest connected cluster > (Tiago de Paula Peixoto) > > > ---------------------------------------------------------------------- > > Message: 1 > Date: Tue, 10 Jun 2014 11:01:39 +0530 > From: Shubham Bhushan <shubphotons(a)gmail.com> > To: graph-tool(a)skewed.de > Subject: [graph-tool] Algorithm to find the largest connected cluster > Message-ID: > <CACpvG2HkeACyDVLhkwUw2= > qxtpj2chR8ROCYostkiPhz+f+HrA(a)mail.gmail.com> > Content-Type: text/plain; charset="utf-8" > > Hi > I want to know what Algorithm Graph Tool uses to find the larges connected > cluster. If possible provide me the links to research paper/book/blog where > the algorithm is discussed. > Shubham > > -- > http://about.me/shubham.bhushan >

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Algorithm to find the largest connected cluster
by Shubham Bhushan 10 Jun '14

10 Jun '14

Hi I want to know what Algorithm Graph Tool uses to find the larges connected cluster. If possible provide me the links to research paper/book/blog where the algorithm is discussed. Shubham -- http://about.me/shubham.bhushan

2 1

Problem on community extraction
by jmazel 07 Jun '14

07 Jun '14

Hi I am trying to extract communities of a graph with the graph_tool.community.minimize_blockmodel_dl function and by following the example on this page: http://graph-tool.skewed.de/static/doc/community.html. Unfortunately, I get an error: Traceback (most recent call last): File "community.py", line 7, in <module> graph_draw(g, pos=g.vp["pos"], vertex_fill_color=b, vertex_shape=b, output="output_blocks_mdl.pdf") File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 995, in __getitem__ val = self.get_func(self.g, key) File "/usr/lib/python2.7/dist-packages/graph_tool/__init__.py", line 1458, in <lambda> lambda g, k: g.__properties[("v", k)], KeyError: ('v', 'pos') Here is my code: from graph_tool.all import * g = load_graph("graph.dot") b, mdl = minimize_blockmodel_dl(g) graph_draw(g, pos=g.vp["pos"], vertex_fill_color=b, vertex_shape=b, output="output_blocks_mdl.pdf") The dot file looks like this: graph G { 167; 2037; 717; 2169; 166; 669; 2541; 1781; 1424; 167 -- 166; 2037 -- 669; 2037 -- 1424; 717 -- 166; 717 -- 167; 2169 -- 669; 2169 -- 2037; 2541 -- 166; 2541 -- 167; 2541 -- 669; 2541 -- 717; 2541 -- 1781; 2541 -- 2037; } Thnaks for your time. -- 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.

3 2

no attribute 'graph_draw'
by jean-patrick 07 Jun '14

07 Jun '14

Hello, graph_tool is installed on ubuntu trusty according to the documentation and when the following code is run from an ipython cell, I have: import graph_tool as gt mG = gt.Graph(directed = False) v1 = mG.add_vertex() v2 = mG.add_vertex() mG.add_edge(v1,v2) print gt.__version__ gt.graph_draw(mG) --------------------------------------------------------------------------- AttributeError Traceback (most recent call last) <ipython-input-4-a81ac2c86e8f> in <module>() 4 mG.add_edge(v1,v2) 5 print gt.__version__ ----> 6 gt.graph_draw(mG) AttributeError: 'module' object has no attribute 'graph_draw' 2.2.30 (commit 8ff4701a, Tue Mar 25 13:40:40 2014 +0100) I also tried to build graph-tool from source but the compilation failed due to a lack of virtual memory (1.22 Go RAM and 1.85 Go swap) Thank you for your advices. Jean-Patrick -- 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.

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graph-tool June 2014