Slices¶

A slice is a named subset of a graph. Think of it as a condition, cohort, or sample label — the network analog of an obs group in AnnData.

A slice membership is two things:

• a set of vertex ids
• a set of edge ids

The same vertex or edge can live in many slices.

In [1]:

from annnet import AnnNet

G = AnnNet(directed=True)
G.add_vertices(['A', 'B', 'C', 'D'])
G.add_edges('A', 'B', edge_id='e1', weight=1.0)
G.add_edges('B', 'C', edge_id='e2', weight=2.0)
G.add_edges('C', 'D', edge_id='e3', weight=3.0)
G

from annnet import AnnNet G = AnnNet(directed=True) G.add_vertices(['A', 'B', 'C', 'D']) G.add_edges('A', 'B', edge_id='e1', weight=1.0) G.add_edges('B', 'C', edge_id='e2', weight=2.0) G.add_edges('C', 'D', edge_id='e3', weight=3.0) G

Out[1]:

AnnNet object with n_vertices × n_edges = 4 × 3
    directed: True
    slices: ['default']

Create slices¶

G.slices.add(name, **attrs) registers a new slice. Slice-level attributes (e.g. cohort label) go in the kwargs.

In [2]:

G.slices.add('control', cohort='wt')
G.slices.add('treated', cohort='ko')
print('slices:', G.slices.list())
print('control attrs:', G.attrs.get_slice_attr('control', 'cohort'))

G.slices.add('control', cohort='wt') G.slices.add('treated', cohort='ko') print('slices:', G.slices.list()) print('control attrs:', G.attrs.get_slice_attr('control', 'cohort'))

slices: ['default', 'control', 'treated']
control attrs: wt

Attach edges and vertices¶

Two ways:

1. Pass slice='name' when calling add_edges (the edge lands in that slice immediately).
2. Call G.slices.add_edges('name', [edge_ids]) after the fact.

Either way, the slice's vertex set grows to include the endpoints.

In [3]:

# Path A: declare at edge creation time
G.add_edges('A', 'D', edge_id='e_short', slice='treated', weight=5.0)

# Path B: assign existing edges to a slice
G.slices.add_edges('control', ['e1', 'e2'])
G.slices.add_edges('treated', ['e2', 'e3', 'e_short'])

print('control edges:', sorted(G.slices.edges('control')))
print('treated edges:', sorted(G.slices.edges('treated')))
print('treated vertices:', sorted(G.slices.vertices('treated')))

# Path A: declare at edge creation time G.add_edges('A', 'D', edge_id='e_short', slice='treated', weight=5.0) # Path B: assign existing edges to a slice G.slices.add_edges('control', ['e1', 'e2']) G.slices.add_edges('treated', ['e2', 'e3', 'e_short']) print('control edges:', sorted(G.slices.edges('control'))) print('treated edges:', sorted(G.slices.edges('treated'))) print('treated vertices:', sorted(G.slices.vertices('treated')))

control edges: ['e1', 'e2']
treated edges: ['e2', 'e3', 'e_short']
treated vertices: ['A', 'B', 'C', 'D']

Slice algebra¶

Combine slices with union, intersect, difference. Each returns a dict of {'vertices': set, 'edges': set}.

In [4]:

both = G.slices.intersect(['control', 'treated'])
print('common edges:', sorted(both['edges']))

either = G.slices.union(['control', 'treated'])
print('union edges:', sorted(either['edges']))

control_only = G.slices.difference('control', 'treated')
print('control-only edges:', sorted(control_only['edges']))

both = G.slices.intersect(['control', 'treated']) print('common edges:', sorted(both['edges'])) either = G.slices.union(['control', 'treated']) print('union edges:', sorted(either['edges'])) control_only = G.slices.difference('control', 'treated') print('control-only edges:', sorted(control_only['edges']))

common edges: ['e2']
union edges: ['e1', 'e2', 'e3', 'e_short']
control-only edges: ['e1']

Per-slice weight overrides¶

A single edge can have different weights in different slices. The base weight lives on the edge; per-slice overrides live on the (slice, edge) pair.

In [5]:

G.attrs.set_edge_slice_attrs('treated', 'e2', weight=99.0)

print('base weight (e2):           ', G.attrs.get_effective_edge_weight('e2'))
print('weight in slice control:    ', G.attrs.get_effective_edge_weight('e2', slice='control'))
print('weight in slice treated:    ', G.attrs.get_effective_edge_weight('e2', slice='treated'))

G.attrs.set_edge_slice_attrs('treated', 'e2', weight=99.0) print('base weight (e2): ', G.attrs.get_effective_edge_weight('e2')) print('weight in slice control: ', G.attrs.get_effective_edge_weight('e2', slice='control')) print('weight in slice treated: ', G.attrs.get_effective_edge_weight('e2', slice='treated'))

base weight (e2):            2.0
weight in slice control:     2.0
weight in slice treated:     99.0

!!! tip "Active slice" G.slices.active returns the currently active slice (default 'default'). When you call get_effective_edge_weight(eid) without a slice=, the active slice is used as fallback.

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Next: 05 — Hyperedges.