You have adjacency matrix in which row.names and col names are your genes. Then you should convert this matrix file to an edge list file: graph_adj=as.data.frame(as.table(as.matrix(net))) write.table(graph_adj, "graph_adj.txt", sep="\t") Now you can open the file in excel, edit it and finally import to cytoscape....

c++,boost,graph,edges,neighbours

1. don't work on a copy bool edgesneighbors(Graph g, edge_iter ep1, edge_iter ep2) This takes g by value, making a copy. Of course, ep1 and ep2 are not valid iterators into the copy Take it by reference: bool edgesneighbors(Graph const& g, edge_iter ep1, edge_iter ep2) { 2. don't use the...

python,list,nodes,networkx,edges

How about this: data = [('"$weepstake$" (1979) {(#1.2)}', '10.0'), ('"\'Til Death Do Us Part" (2006) {Pilot(#1.0)}', '3.7'), ('"\'Conversations with My Wife\'" (2010)', '4.2'), ('"\'Da Kink in My Hair" (2007)', '4.2')] import networkx as nx G = nx.Graph() G.add_edges_from(data) nx.draw(G) if you want a count of edges from a score. len(G.edges('4.2'))...

python,time-complexity,igraph,edges

What you do is perfectly fine; maybe the for loop could be replaced with a zip call. If you are using Python 2.x:: from itertools import izip edges, weights = izip(*dict_edges.iteritems()) g = Graph(edges, edge_attrs={"weight": weights}) If you are using Python 3.x:: edges, weights = zip(*dict_edges.items()) g = Graph(edges, edge_attrs={"weight":...

Maybe you want something like this: library(igraph) library(Matrix) download.file("https://www.dropbox.com/s/q7sxfwjec97qzcy/people.csv?dl=1", tf <- tempfile(fileext = ".csv"), mode = "wb") people <- read.csv(tf) A <- spMatrix(nrow = length(unique(people$people)), ncol = length(unique(people$repository_id)), i = as.numeric(factor(people$people)), j = as.numeric(factor(people$repository_id)), x = rep(1, length(as.numeric(people$people))) ) row.names(A) <- levels(factor(people$people)) colnames(A) <-...

algorithm,depth-first-search,edges

Your relationships for forward and back edges are incorrect - you should exchange them. Apart from that, I would recommend reading this paragraph from wikipedia: http://en.wikipedia.org/wiki/Depth-first_search#Output_of_a_depth-first_search it includes a more intuitive and straightforward definition of those edges and a good picture: Direct answers to your questions When we have for...

java,graph,nodes,stanford-nlp,edges

Here's a basic example of forming the edge list. (The node list part should be easy — you just need to iterate over the tokens in the sentence and print them out.) SemanticGraph sg = .... for (SemanticGraphEdge edge : sg.getEdgesIterable()) { int headIndex = edge.getGovernor().index(); int depIndex = edge.getDependent().index();...

python,text,dictionary,graph,edges

As one other possible option, you can also use defaultdict here: from collections import defaultdict d = defaultdict(list) with open("/Volumes/City_University/data_mining/Ecoli.txt") as f: for line in f: key, val = line.split() d[key].append(val) for k, v in d.items(): print(k, v) This saves you from having to check whether a key is already...

These are the very basic functionalities of igraph, described here thoroughly. If you iterate the <EdgeSeq> object (graph.es), you will go through all <Edge> objects (here edge). <Edge> has properties source and target. These are vertex ids, simply integers. You can get the corresponding <Vertex> object by graph.vs[]: for edge...

Here's the way I would solve it, using your code from above to create the g object. This was trickier than at first glance because of the multi-color membership at the group/connectedness/cluster level that you wanted to attain.: ## Find cluster membership: c <- clusters(g) d <- data.frame(membership=c$membership, color=V(g)$color, id=1:length(V(g)))...

Just repeating my comment... Adj(i,j) = 1 tells you there is an edge connecting nodes i and j. If A(i,j) = 1 then A(j,i) = 1 as well, as these indicate the same edge. Since we count every edge twice, we need to divide the total by 2....

There are classes you can use in your stylesheet for this purpose. They will take on the style specified in the stylesheet, regardless of when they are created -- similar to CSS stylesheets in HTML.

csv,neo4j,cypher,graph-databases,edges

First of all, make sure that you have indexes on the property CSN of the Customer Label. This can be a simple index or I guess in your case a unique constraint. Secondly, I propose to run first a small import of 10 lines and analyse what the execution plan...

python,list,graph,vertices,edges

You can zip your two lists, then use itertools.product to create each of your combinations. You can use itertools.chain.from_iterable to flatten the resulting list. >>> import itertools >>> List1 = [ ['a','b'], ['c','d','e'], ['f'] ] >>> List2 = [ ['g','h','i'], ['j'], ['k','l'] ] >>> list(itertools.chain.from_iterable(itertools.product(a,b) for a,b in zip(List1, List2)))...

javascript,jquery,graph,cytoscape.js,edges

The solution to this issue is at git_cytoscapejs_issues_779

graph,apache-spark,vertices,edges,spark-graphx

Try: edges.intersection(edges.map(e => Edge(e.dstId, e.srcId)) Note that this compares the Edge.attr values as well. If you want to ignore attr values, then do this: edges.map(e=> (e.srcId,e.dstId)).intersection(edges.map(e => (e.dstId, e.srcId))) ...

Answering the updated question There are a few issues with putting Nodes directly in a std::vector in your case. Using a std::vector is great for many things, but if you are doing that, you should make sure not to take pointers to vectors. Remember, pointers refer to exact addresses in...