API overview

Import annnet as:

import annnet as an

All names below are in the top-level annnet namespace, unless the name shows a subpackage. A name that is not on this page or on the page of its object is internal: for example a name that begins with an underscore, or a module such as annnet.core._store. Internal names can change without notice.

Graph

name	description
AnnNet	The graph object. Graph is the same class.
GraphView	A live, read-only view of a graph, from anet.view(...).
annnet.core.NodeSequence, annnet.core.EdgeSequence	The nodes and edges, anet.N and anet.E, and the selections made from them.
NodeView, EdgeView	One node or one edge, from anet.N.at(id) and anet.E.at(id).
Endpoint, as_endpoint, as_endpoints	One side of an edge: the node and its layer.
Provenance	The sources that a graph was built from, anet.provenance.

Attributes

name	description
Attrs	All attributes of a graph, anet.attrs.
RowSelection	The rows that anet.attrs.select and anet.attrs.from_frame select.
Schema	The keys and fields of one attribute address.

Slices and layers

name	description
anet.slices	Named subsets of the edges and nodes.
anet.layers	Aspects, layers and node placements of a multilayer graph.
Aspect, OrderedLabels, as_aspect	One aspect and the order of its labels.
LayerSelection	The layers that one window names.
ValueMatrix, MatrixValues, ValueResolver	Values of nodes on layers, held as arrays.

Other namespaces of the graph

name	description
anet.nx, anet.ig, anet.gt	Algorithms of NetworkX, igraph and graph-tool on the graph.
anet.ops	Copy, subgraph, union, intersection, difference.
anet.idx	IDs to matrix positions, and back.
anet.cache	Cached sparse matrices.
anet.history	A log of changes, and snapshots.

Reading and writing

name	description
read, write	The native .annnet format.
from_edge_frame, add_edges_from_frame, edge_id_for	A graph from a table of edges.
from_dataframes, to_dataframes	A graph as a set of tables.
from_parquet, to_parquet	A directory of Parquet tables.
from_csv, from_dataframe, to_csv, edges_to_csv, hyperedges_to_csv	CSV files.
from_excel, to_excel	Excel workbooks.
from_json, to_json, read_ndjson, write_ndjson	JSON and NDJSON.
from_graphml, to_graphml, from_gexf, to_gexf	GraphML and GEXF files.
from_sif, to_sif	Simple Interaction Format.
from_sbml, to_sbml, from_sbml_cobra, from_cobra_model	SBML models.
from_cx2, to_cx2	Cytoscape CX2.
from_pyg, to_pyg	PyTorch Geometric.

What each format keeps compares the formats.

Other graph libraries

name	description
from_nx, to_nx	NetworkX graphs.
from_igraph, to_igraph	igraph graphs.
from_graphtool, to_graphtool	graph-tool graphs.
available_backends	The graph libraries that are installed.

Algorithms

name	description
sources, targets, directed_pairs, directed_cycle	Facts about the directed edges.

Plotting

name	description
annnet.utils.plot, annnet.utils.save, annnet.utils.show_cytoscape	Draw a graph, write the drawing to a file, or show the graph as an interactive network.

Package and settings

name	description
info, __version__, get_latest_version	The package version and its optional components.
set_default_dataframe_backend and others	The dataframe library for new tables.
set_default_plot_backend and others	The plotting library.

Errors

annnet raises the standard Python exceptions, with a message that names the problem:

situation	exception
An unknown node, edge, slice, aspect, layer or attribute key.	KeyError
A key or argument of the wrong shape or type. A predicate that compares values that cannot be compared. A node selection given where edges are expected.	TypeError
A reserved field. A key that occurs two times in one batch. A missing or null key column. delete without keys and without names. An ordering operator on a categorical aspect. A selection from another graph. A bad boundary, limit, layout or operator.	ValueError
A write through a view.	ReadOnlyViewError, a subclass of TypeError
A name that annnet removed.	AttributeError, with the name to use instead