Slices and Multilayer Workflows¶

AnnNet has two related organizational concepts:

• slices: named subsets of graph membership, useful for conditions, experiments, or time points
• layers: Kivela-style multilayer structure, useful when vertices can exist in several aspect combinations

This notebook shows how they relate and how to move between them.

In [1]:

from pathlib import Path
import sys

NOTEBOOK_DIR = Path.cwd()
PACKAGE_ROOT = (NOTEBOOK_DIR / "..").resolve()
if str(PACKAGE_ROOT) not in sys.path:
    sys.path.insert(0, str(PACKAGE_ROOT))

import annnet as an

from pathlib import Path import sys NOTEBOOK_DIR = Path.cwd() PACKAGE_ROOT = (NOTEBOOK_DIR / "..").resolve() if str(PACKAGE_ROOT) not in sys.path: sys.path.insert(0, str(PACKAGE_ROOT)) import annnet as an

In [2]:

G = an.AnnNet(directed=True)
G.add_vertices(["TP53", "MDM2", "BAX", "ATM"])

G.slices.add("baseline", condition="baseline")
G.slices.add("treated", condition="dna_damage")

G.add_edge("ATM", "TP53", slice="treated", edge_id="damage_sensing")
G.add_edge("TP53", "MDM2", slice="baseline", edge_id="feedback_baseline")
G.add_edge("TP53", "BAX", slice="treated", edge_id="apoptosis_program")

G = an.AnnNet(directed=True) G.add_vertices(["TP53", "MDM2", "BAX", "ATM"]) G.slices.add("baseline", condition="baseline") G.slices.add("treated", condition="dna_damage") G.add_edge("ATM", "TP53", slice="treated", edge_id="damage_sensing") G.add_edge("TP53", "MDM2", slice="baseline", edge_id="feedback_baseline") G.add_edge("TP53", "BAX", slice="treated", edge_id="apoptosis_program")

Out[2]:

'apoptosis_program'

In [3]:

print("active slice:", G.slices.active)
print("slices:", G.slices.list(include_default=True))
print("treated info:", G.slices.info("treated"))
print("treated edges:", G.slices.edges("treated"))
G.slices_view()

print("active slice:", G.slices.active) print("slices:", G.slices.list(include_default=True)) print("treated info:", G.slices.info("treated")) print("treated edges:", G.slices.edges("treated")) G.slices_view()

active slice: default
slices: ['default', 'baseline', 'treated']
treated info: {'vertices': {'ATM', 'TP53', 'BAX'}, 'edges': {'damage_sensing', 'apoptosis_program'}, 'attributes': {'condition': 'dna_damage'}}
treated edges: {'damage_sensing', 'apoptosis_program'}

Out[3]:

shape: (2, 2)

slice_id	condition
str	str
"baseline"	"baseline"
"treated"	"dna_damage"

In [4]:

G.slices.union(["baseline", "treated"])

G.slices.union(["baseline", "treated"])

Out[4]:

{'vertices': {'ATM', 'BAX', 'MDM2', 'TP53'},
 'edges': {'apoptosis_program', 'damage_sensing', 'feedback_baseline'}}

Configure a single-aspect multilayer structure¶

Here the aspect is condition, with two elementary layers: baseline and treated.

In [5]:

G.set_aspects(["condition"], {"condition": ["baseline", "treated"]})

for layer in [("baseline",), ("treated",)]:
    for vertex in ["TP53", "MDM2", "BAX", "ATM"]:
        G.add_presence(vertex, layer)

G.add_intra_edge("TP53", "MDM2", "baseline", eid="ml_feedback")
G.add_intra_edge("TP53", "BAX", "treated", eid="ml_apoptosis")
G.add_inter_edge("TP53", "TP53", "baseline", "treated", eid="tp53_state_transfer")

G.set_aspects(["condition"], {"condition": ["baseline", "treated"]}) for layer in [("baseline",), ("treated",)]: for vertex in ["TP53", "MDM2", "BAX", "ATM"]: G.add_presence(vertex, layer) G.add_intra_edge("TP53", "MDM2", "baseline", eid="ml_feedback") G.add_intra_edge("TP53", "BAX", "treated", eid="ml_apoptosis") G.add_inter_edge("TP53", "TP53", "baseline", "treated", eid="tp53_state_transfer")

Out[5]:

'tp53_state_transfer'

In [6]:

print("aspects:", G.layers.aspects())
print("elementary layers:", G.layers.elementary_layers())
print("layer tuples:", G.layers.layer_tuples())
print("baseline vertices:", G.layers.vertex_set(("baseline",)))
print("baseline edges:", G.layers.edge_set(("baseline",), include_inter=True))

print("aspects:", G.layers.aspects()) print("elementary layers:", G.layers.elementary_layers()) print("layer tuples:", G.layers.layer_tuples()) print("baseline vertices:", G.layers.vertex_set(("baseline",))) print("baseline edges:", G.layers.edge_set(("baseline",), include_inter=True))

aspects: ['condition']
elementary layers: {'condition': ['baseline', 'treated']}
layer tuples: [('baseline',), ('treated',)]
baseline vertices: {'TP53', 'ATM', 'MDM2', 'BAX'}
baseline edges: {'tp53_state_transfer', 'ml_feedback'}

In [7]:

G.layers.to_slice(("treated",), slice_id="treated_from_layers", source="layers API")
print(G.slices.info("treated_from_layers"))

G.layers.to_slice(("treated",), slice_id="treated_from_layers", source="layers API") print(G.slices.info("treated_from_layers"))

{'vertices': {'TP53', 'ATM', 'MDM2', 'BAX'}, 'edges': {'ml_apoptosis'}, 'attributes': {'source': 'layers API', 'layer_tuple': ('treated',)}}

In [8]:

A = G.layers.supra_adjacency()
print(type(A).__name__)
print(A.shape)

A = G.layers.supra_adjacency() print(type(A).__name__) print(A.shape)

csr_matrix
(8, 8)

In [ ]: