- Python Advanced Course Topics
- Creating Graphs in Python using Networkx
- An Intro to Graph Theory
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- Python Advanced Course Topics
Python Advanced Course Topics
By definition, a Graph is a collection of nodes vertices along with identified pairs of nodes called edges, links, etc. In NetworkX, nodes can be any hashable object e. The graph G can be grown in several ways. NetworkX includes many graph generator functions and facilities to read and write graphs in many formats. You can add one node at a time. Node attributes are discussed further below. Note that G now contains the nodes of H as nodes of G. In contrast, you could use the graph H as a node in G. The graph G now contains H as a node. This flexibility is very powerful as it allows graphs of graphs, graphs of files, graphs of functions and much more. It is worth thinking about how to structure your application so that the nodes are useful entities. Of course you can always use a unique identifier in G and have a separate dictionary keyed by identifier to the node information if you prefer. G can also be grown by adding one edge at a time. An ebunch is any iterable container of edge-tuples. An edge-tuple can be a 2-tuple of nodes or a 3-tuple with 2 nodes followed by an edge attribute dictionary, e. Edge attributes are discussed further below. There are no complaints when adding existing nodes or edges. For example, after removing all nodes and edges. At this stage the graph G consists of 8 nodes and 3 edges, as can be seen by:. We can examine the nodes and edges. Four basic graph properties facilitate reporting: G. These are set-like views of the nodes, edges, neighbors adjacenciesand degrees of nodes in a graph. They offer a continually updated read-only view into the graph structure. They are also dict-like in that you can look up node and edge data attributes via the views and iterate with data attributes using methods. If you want a specific container type instead of a view, you can specify one. Here we use lists, though sets, dicts, tuples and other containers may be better in other contexts.Creating Graphs in Python using Networkx
By definition, a Graph is a collection of nodes vertices along with identified pairs of nodes called edges, links, etc. In NetworkX, nodes can be any hashable object e. The graph G can be grown in several ways. NetworkX includes many graph generator functions and facilities to read and write graphs in many formats. You can add one node at a time. An nbunch is any iterable container of nodes that is not itself a node in the graph. Note that G now contains the nodes of H as nodes of G. In contrast, you could use the graph H as a node in G. The graph G now contains H as a node. This flexibility is very powerful as it allows graphs of graphs, graphs of files, graphs of functions and much more. It is worth thinking about how to structure your application so that the nodes are useful entities. Of course you can always use a unique identifier in G and have a separate dictionary keyed by identifier to the node information if you prefer. Note: You should not change the node object if the hash depends on its contents. An ebunch is any iterable container of edge-tuples. An edge-tuple can be a 2-tuple of nodes or a 3-tuple with 2 nodes followed by an edge attribute dictionary, e. Edge attributes are discussed further below. One can demolish the graph in a similar fashion; using Graph. There are no complaints when adding existing nodes or edges. For example, after removing all nodes and edges. When creating a graph structure by instantiating one of the graph classes you can specify data in several formats. You might notice that nodes and edges are not specified as NetworkX objects. This leaves you free to use meaningful items as nodes and edges. The most common choices are numbers or strings, but a node can be any hashable object except Noneand an edge can be associated with any object x using G. As an example, n1 and n2 could be protein objects from the RCSB Protein Data Bank, and x could refer to an XML record of publications detailing experimental observations of their interaction. We have found this power quite useful, but its abuse can lead to unexpected surprises unless one is familiar with Python. In addition to the methods Graph. Do not change the returned dict—it is part of the graph data structure and direct manipulation may leave the graph in an inconsistent state. You can safely set the attributes of an edge using subscript notation if the edge already exists. Fast examination of all edges is achieved using adjacency iterators. Note that for undirected graphs this actually looks at each edge twice.
An Intro to Graph Theory
By convention None is not used as a node. If None default an empty graph is created. Add the nodes from any container a list, dict, set or even the lines from a file or the nodes from another graph. In addition to strings and integers any hashable Python object except None can represent a node, e. If some edges connect nodes not yet in the graph, the nodes are added automatically. There are no errors when adding nodes or edges that already exist. Warning: we protect the graph data structure by making G. However, you can assign to attributes in e. Often the best way to traverse all edges of a graph is via the neighbors. The neighbors are reported as an adjacency-dict G. Simple graph information is obtained using object-attributes and methods. Reporting usually provides views instead of containers to reduce memory usage. The views update as the graph is updated similarly to dict-views. The Graph class uses a dict-of-dict-of-dict data structure. Each of these three dicts can be replaced in a subclass by a user defined dict-like object. In general, the dict-like features should be maintained but extra features can be added. To replace one of the dicts create a new graph class by changing the class! Factory function to be used to create the dict containing node attributes, keyed by node id. It should require no arguments and return a dict-like object. Factory function to be used to create the node attribute dict which holds attribute values keyed by attribute name. Factory function to be used to create the outer-most dict in the data structure that holds adjacency info keyed by node. Factory function to be used to create the adjacency list dict which holds edge data keyed by neighbor. Factory function to be used to create the edge attribute dict which holds attribute values keyed by attribute name. Factory function to be used to create the graph attribute dict which holds attribute values keyed by attribute name. To facilitate this we define two class variables that you can set in your subclass. Create a low memory graph class that effectively disallows edge attributes by using a single attribute dict for all edges. This reduces the memory used, but you lose edge attributes. Please see ordered for more examples of creating graph subclasses by overwriting the base class dict with a dictionary-like object. Returns a SubGraph view of the subgraph induced on nodes.
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By convention None is not used as a node. If None default an empty graph is created. Add the nodes from any container a list, dict, set or even the lines from a file or the nodes from another graph. In addition to strings and integers any hashable Python object except None can represent a node, e. If some edges connect nodes not yet in the graph, the nodes are added automatically. There are no errors when adding nodes or edges that already exist. Warning: we protect the graph data structure by making G. However, you can assign to attributes in e. Often the best way to traverse all edges of a graph is via the neighbors. The neighbors are reported as an adjacency-dict G. Simple graph information is obtained using object-attributes and methods. Reporting typically provides views instead of containers to reduce memory usage. The views update as the graph is updated similarly to dict-views. The Graph class uses a dict-of-dict-of-dict data structure. Each of these three dicts can be replaced in a subclass by a user defined dict-like object. In general, the dict-like features should be maintained but extra features can be added. To replace one of the dicts create a new graph class by changing the class! Factory function to be used to create the dict containing node attributes, keyed by node id. It should require no arguments and return a dict-like object. Factory function to be used to create the node attribute dict which holds attribute values keyed by attribute name. Factory function to be used to create the outer-most dict in the data structure that holds adjacency info keyed by node. Factory function to be used to create the adjacency list dict which holds edge data keyed by neighbor.
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