graph-tool August 2018

graph-tool@skewed.de

4 participants
11 discussions

How to control the orientation of the graph topology
by Xun Xiao 26 Feb '22

26 Feb '22

Hi Tiago, sometimes, when delete the graph and create a new one, then plot it, the plotted graph is shown upside down (in terms of the node text). So how could we control the orientation of the graph? Or which parameter we should use to always make node text shown in a correct orientation. Thanks a lot. -- 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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Upside down labels
by charlie 26 Feb '22

26 Feb '22

Hi, I'm suffering from the same issue mentioned in this post: https://git.skewed.de/count0/graph-tool/issues/174 Namely, I'm trying to draw a graph that includes a lot of self-looping edges, and my labels are being printed upside down. If I remove the self-loops the labels are shown the right way up. Is there a fix for it? Thanks, Charlie -- 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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What formula is used for std in vertex_average and edge_average?
by VaSa 16 Jul '20

16 Jul '20

I am curious what is being used to calculate the standard deviation of the average in gt.vertex_average and gt.edge_average >>> t2=gt.Graph() >>> t2.add_vertex(2) >>> t2.add_edge(t2.vertex(0), t2.vertex(1)) >>> gt.vertex_average(t2, "in") (0.5, 0.35355339059327373) Now, shouldn't std be σ(n)=sqrt(((0-0.5)^2+(1-0.5)^2)/2)=0.5 ? also q(n-1)=sqrt((0.5^2+0.5^2)/(2-1))~=0.70710 0.3535 is sqrt(2)/4 which happens to be σ(n-1)/2, so it seems there is some relation to that. A little bigger graph. >>> t3=gt.Graph() >>> t3.add_vertex(5) >>> t3.add_edge(t3.vertex(0), t3.vertex(1)) >>> gt.vertex_average(t3, "in") (0.2, 0.17888543819998318) Now, we should have 0,1,0,0,0 series for vertex incoming degree. So Windows calc gives σ(n)=0.4 and σ(n-1)~=0.44721, so where does 0.1788854 come from ? Reason, I am asking because, I have a large graph, where the average looks quite alright but the std makes no sense, as going by the histogram, degree values are quite a bit more distributed than the std would indicate. -- 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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assigning vertex properties when adding edges
by m jadidi 04 Mar '20

04 Mar '20

Hi, I was wondering if there is any way to assign vertex properties while adding edges to the graph. for example using "add_edge_list" I can assign edge properties but later I have to iterate through all vertices again to assign their properties. I know this is not a problem when the vertex property is of the type "int" or "float" because then one can use "vprop.a = values", but in case of "string" and "object" this method doesn't work What would be the best/fastest way to handle this situation. I guess it would be very helpful to extend the "add_edge_list" function to accept vertex property in some way. cheers, -- Mohsen

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Nested Block State hierarchy level after mcmc_equilibrate
by ilyco 16 Jan '20

16 Jan '20

I ran mcmc_equilibrate on a nested block state model in a weighted graph. As per instructions, I copied the initially computed state in another object with increased hierarchy depth to 10. However, this fixed the depth to 10. Everything computed afterwards has depth 10 even if is clear that after 3 or 4 levels the nodes converge to one. There are many empty branches and when I try to plot it with empty_branches = False, I get an error stating it is not a tree. RuntimeError: Invalid hierarchical tree: No path from source to target. Did anybody perform any similar analyses? The hierarchy after mcmc_equilibrate: <NestedBlockState object, with base <BlockState object with 24 blocks (24 nonempty), degree-corrected, with 1 edge covariate, for graph <Graph object, undirected, with 230 vertices and 11230 edges, edges filtered by (<PropertyMap object with key type 'Edge' and value type 'bool', for Graph 0x7fc3a89f1210, at 0x7fc3a64911d0>, False), vertices filtered by (<PropertyMap object with key type 'Vertex' and value type 'bool', for Graph 0x7fc3a89f1210, at 0x7fc3a64912d0>, False) at 0x7fc3a89f1210>, at 0x7fc3a6491950>, and 10 levels of sizes [(230, 24), (24, 5), (5, 1), (1, 1), (1, 1), (1, 1), (1, 1), (1, 1), (1, 1), (1, 1)] at 0x7fc3a6491590> -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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overlapping in nestedmodel
by fanzheng10 29 Oct '18

29 Oct '18

Hi, I am trying to enable overlap in the nested_blockmodel: state = gt.inference.minimize.minimize_nested_blockmodel_dl(g, overlap=True) So far, I have only tried a very simple network ("celegansneural"), and it gives me three levels, with the first level being a OverlapBlockState and upper levels being BlockState. [<OverlapBlockState object with 3 blocks, degree corrected, for graph <Graph object, directed, with 297 vertices and 2359 edges at 0x10bc7d710>, at 0x1351e6470>, <BlockState object with 2 blocks (2 nonempty), for graph <Graph object, directed, with 3 vertices and 6 edges at 0x135e3a1d0>, at 0x135e27ac8>, <BlockState object with 1 blocks (1 nonempty), for graph <Graph object, directed, with 2 vertices and 3 edges at 0x135214128>, at 0x1352192b0>] I am interested in inferred a DAG structure from some networks, i.e. not only the leaf nodes, but nodes on intermediate level can have multiple membership. I am wondering whether the fact that I only get one level of overlapping block is due to the very simple network, or is it simply not possible to have multiple levels of overlapping blocks? -- Sent from: http://main-discussion-list-for-the-graph-tool-project.982480.n3.nabble.com/

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Problem with add_edge_list(eprop=x)
by JHickey 04 Oct '18

04 Oct '18

I'd like to use the "add_edge_list" function to add edges to my graph, and simultaneously assign a value for an edge property map for each of the added edges. When I try the following example (with no edge property map information) works fine: elist1 = np.array([[0,1], [1, 2]]) #edge list with no value for edge property map data (only the source and target for the edges) g = gt.Graph() my_eprop = g.new_edge_property('bool') g.add_edge_list(elist) But with the following example, I get the error below: elist2 = np.array([[0,1, 1], [1, 2, 0]]) #edge list with edge property map value in 3rd column g = gt.Graph() my_eprop = g.new_edge_property('bool') g.add_edge_list(elist2, eprops=my_eprop) Error: --------------------------------------------------------------------------- ValueError Traceback (most recent call last) <ipython-input-48-6a949ea52c9b> in <module>() ----> 1 g.add_edge_list(elist2, eprops=my_eprop) /usr/lib/python2.7/dist-packages/graph_tool/__init__.pyc in add_edge_list(self, edge_list, hashed, string_vals, eprops) 1969 eprops = () 1970 else: -> 1971 convert = [_converter(x.value_type()) for x in eprops] 1972 eprops = [_prop("e", self, x) for x in eprops] 1973 if not isinstance(edge_list, numpy.ndarray): /usr/lib/python2.7/dist-packages/graph_tool/__init__.pyc in __getitem__(self, k) 534 kt = "Graph" 535 raise ValueError("invalid key '%s' of type '%s', wanted type: %s" --> 536 % (str(k), str(type(k)), kt) ) 537 538 def __setitem__(self, k, v): ValueError: invalid key '0' of type '<type 'int'>', wanted type: Edge --------------------------------------------------------------------------- Please help! -- 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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(no subject)
by Zahra Sheikhbahaee 26 Sep '18

26 Sep '18

Hi Tiago, I installed graph-tool on a mac machine. After struggling a lot to import graph_tool without any error in python, I was running an example with plotting and I was getting following error >>> from graph_tool import all /Users/zahra/anaconda3/lib/python3.6/site-packages/graph_tool/draw/cairo_draw.py:1494: RuntimeWarning: Error importing Gtk module: No module named 'gi'; GTK+ drawing will not work. warnings.warn(msg, RuntimeWarning) >>> from graph_tool.all import * >>> g=Graph() >>> v1 = g.add_vertex( ... ) >>> v2 = g.add_vertex() >>> e=g.add_edge(v1,v2) >>> graph_draw(g, vertex_text=g.vertex_index, vertex_font_size=18,output_size=(200, 200), output="../two-nodes.png") Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/Users/zahra/anaconda3/lib/python3.6/site-packages/graph_tool/draw/cairo_draw.py", line 1185, in graph_draw nodesfirst, fit_view=fit_view, **kwargs) File "/Users/zahra/anaconda3/lib/python3.6/site-packages/graph_tool/draw/cairo_draw.py", line 707, in cairo_draw max_render_time, cr) MemoryError >>> quit() Well, googling this error did not help to solve the problem. Could you please suggest a solution ? Thanks in advance. Cheers, Zahra

2 1

Viewing the gt.collection.data as a pandas Dataframe
by Rachit Saluja 06 Aug '18

06 Aug '18

Hello, I have recently started working with graph-tool, and was wondering if we can try to view any of the data provided in the repo as a pandas Dataframe? This would be helpful, because I would like to analyze a few things with a custom dataset. For example, gt.collection.data["celegansneural"], can it be displayed as a dataframe? Or any other way? I would like to see the all the content in it. Warm regards, Rachit Saluja

2 1

find_edge_range issue in version 2.7?
by Hobé Alex 06 Aug '18

06 Aug '18

Hi there! Due to certain limitations, we are trying to install the graphtool version 2.7 on a redhat distribution. After a lot of fidling around, we have been able to make the functions we need work, except for the find_edge_range function. The following simple example demonstrates the problem: from graph_tool.all import * g = Graph() v1, v2 = g.add_vertex(), g.add_vertex() e1,e2 = g.add_edge(v1,v2), g.add_edge(v2,v1) res = g.new_edge_property("double") res[e1] = 0.1 res[e2] = 12. eList = find_edge_range(g,res, [0.0, 1.]) This causes the following issue: Traceback (most recent call last): File "<stdin>", line 1, in <module> File "/graph_tool/util/__init__.py", line 84, in find_edge_range convert = converter(prop.value_type()) NameError: global name 'converter' is not defined Unfortunately, I have not found a way to see the actual code, where this error arises. Was this a problem in that particular version? What do I need to do to find the code where this issue arises? The following python loop is able to reproduce the desired behavior, but it is way too slow: eList = [] for e in g.edges(): if res[e] <= eps and res[e] >= 0.0: eList.append(e) Is there a more efficient way to do this, if I cannot make "find_edge_range" work? Looking forward to hearing from you. All the best, Alex

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graph-tool August 2018