risk-network 0.0.8b18__py3-none-any.whl → 0.0.9b26__py3-none-any.whl
This diff represents the content of publicly available package versions that have been released to one of the supported registries. The information contained in this diff is provided for informational purposes only and reflects changes between package versions as they appear in their respective public registries.
- risk/__init__.py +2 -2
- risk/annotations/__init__.py +2 -2
- risk/annotations/annotations.py +133 -72
- risk/annotations/io.py +50 -34
- risk/log/__init__.py +4 -2
- risk/log/{config.py → console.py} +5 -3
- risk/log/{params.py → parameters.py} +21 -46
- risk/neighborhoods/__init__.py +3 -5
- risk/neighborhoods/api.py +446 -0
- risk/neighborhoods/community.py +281 -96
- risk/neighborhoods/domains.py +92 -38
- risk/neighborhoods/neighborhoods.py +210 -149
- risk/network/__init__.py +1 -3
- risk/network/geometry.py +69 -58
- risk/network/graph/__init__.py +6 -0
- risk/network/graph/api.py +194 -0
- risk/network/graph/network.py +269 -0
- risk/network/graph/summary.py +254 -0
- risk/network/io.py +58 -48
- risk/network/plotter/__init__.py +6 -0
- risk/network/plotter/api.py +54 -0
- risk/network/{plot → plotter}/canvas.py +80 -26
- risk/network/{plot → plotter}/contour.py +43 -34
- risk/network/{plot → plotter}/labels.py +123 -113
- risk/network/plotter/network.py +424 -0
- risk/network/plotter/utils/colors.py +416 -0
- risk/network/plotter/utils/layout.py +94 -0
- risk/risk.py +11 -469
- risk/stats/__init__.py +8 -4
- risk/stats/binom.py +51 -0
- risk/stats/chi2.py +69 -0
- risk/stats/hypergeom.py +28 -18
- risk/stats/permutation/__init__.py +1 -1
- risk/stats/permutation/permutation.py +45 -39
- risk/stats/permutation/test_functions.py +25 -17
- risk/stats/poisson.py +17 -11
- risk/stats/stats.py +20 -16
- risk/stats/zscore.py +68 -0
- {risk_network-0.0.8b18.dist-info → risk_network-0.0.9b26.dist-info}/METADATA +9 -5
- risk_network-0.0.9b26.dist-info/RECORD +44 -0
- {risk_network-0.0.8b18.dist-info → risk_network-0.0.9b26.dist-info}/WHEEL +1 -1
- risk/network/graph.py +0 -159
- risk/network/plot/__init__.py +0 -6
- risk/network/plot/network.py +0 -282
- risk/network/plot/plotter.py +0 -137
- risk/network/plot/utils/color.py +0 -353
- risk/network/plot/utils/layout.py +0 -53
- risk_network-0.0.8b18.dist-info/RECORD +0 -37
- {risk_network-0.0.8b18.dist-info → risk_network-0.0.9b26.dist-info}/LICENSE +0 -0
- {risk_network-0.0.8b18.dist-info → risk_network-0.0.9b26.dist-info}/top_level.txt +0 -0
risk/network/geometry.py
CHANGED
@@ -3,6 +3,8 @@ risk/network/geometry
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~~~~~~~~~~~~~~~~~~~~~
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"""
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import copy
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import networkx as nx
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import numpy as np
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@@ -25,54 +27,50 @@ def assign_edge_lengths(
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nx.Graph: The graph with applied edge lengths.
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"""
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def
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"""Compute the distance between two coordinate vectors.
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Args:
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u_coords (np.ndarray): Coordinates of the first point.
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v_coords (np.ndarray): Coordinates of the second point.
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is_sphere (bool, optional): If True, compute spherical distance. Defaults to False.
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Returns:
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float: The computed distance between the two points.
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"""
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def compute_distance_vectorized(coords, is_sphere):
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"""Compute distances between pairs of coordinates."""
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u_coords, v_coords = coords[:, 0, :], coords[:, 1, :]
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if is_sphere:
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u_norm = np.linalg.norm(u_coords, axis=1, keepdims=True)
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v_norm = np.linalg.norm(v_coords, axis=1, keepdims=True)
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u_coords /= u_norm
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v_coords /= v_norm
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dot_products = np.einsum("ij,ij->i", u_coords, v_coords)
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return np.arccos(np.clip(dot_products, -1.0, 1.0))
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return np.linalg.norm(u_coords - v_coords, axis=1)
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# Normalize graph coordinates
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# Normalize graph coordinates and weights
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_normalize_graph_coordinates(G)
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# Normalize weights
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_normalize_weights(G)
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#
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# Map nodes to sphere and adjust depth if required
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if compute_sphere:
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# Map to sphere and adjust depth
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_map_to_sphere(G)
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G_depth = _create_depth(
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G_depth = _create_depth(copy.deepcopy(G), surface_depth=surface_depth)
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else:
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G_depth = G.copy()
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G_depth = copy.deepcopy(G)
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# Precompute edge coordinate arrays for vectorized computation
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edge_data = []
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for u, v in G_depth.edges:
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u_coords = np.array([G_depth.nodes[u]["x"], G_depth.nodes[u]["y"]])
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v_coords = np.array([G_depth.nodes[v]["x"], G_depth.nodes[v]["y"]])
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if compute_sphere:
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u_coords = np.append(u_coords, G_depth.nodes[u].get("z", 0))
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v_coords = np.append(v_coords, G_depth.nodes[v].get("z", 0))
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edge_data.append([u_coords, v_coords, (u, v)])
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# Convert to numpy for faster processing
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edge_coords = np.array([(e[0], e[1]) for e in edge_data])
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edge_indices = [e[2] for e in edge_data]
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# Compute distances in bulk
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distances = compute_distance_vectorized(edge_coords, compute_sphere)
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# Assign distances back to the graph
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for (u, v), distance in zip(edge_indices, distances):
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if include_edge_weight:
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G.edges[u, v]["length"] = distance / np.sqrt(
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weight = G.edges[u, v].get("normalized_weight", 0) + 1e-6
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G.edges[u, v]["length"] = distance / np.sqrt(weight)
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else:
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# Use calculated distance directly
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G.edges[u, v]["length"] = distance
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return G
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Args:
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G (nx.Graph): The input graph with nodes having 'x' and 'y' coordinates.
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"""
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# Extract x, y coordinates
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# Extract x, y coordinates as a NumPy array
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nodes = list(G.nodes)
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xy_coords = np.array([[G.nodes[node]["x"], G.nodes[node]["y"]] for node in nodes])
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# Normalize coordinates between [0, 1]
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min_vals = xy_coords.min(axis=0)
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max_vals = xy_coords.max(axis=0)
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normalized_xy = (xy_coords - min_vals) / (max_vals - min_vals)
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#
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# Convert normalized coordinates to spherical coordinates
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theta = normalized_xy[:, 0] * np.pi * 2
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phi = normalized_xy[:, 1] * np.pi
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#
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G.nodes[node]["z"] = z
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# Compute 3D Cartesian coordinates
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x = np.sin(phi) * np.cos(theta)
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y = np.sin(phi) * np.sin(theta)
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z = np.cos(phi)
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# Assign coordinates back to graph nodes in bulk
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xyz_coords = {node: {"x": x[i], "y": y[i], "z": z[i]} for i, node in enumerate(nodes)}
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nx.set_node_attributes(G, xyz_coords)
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def _normalize_graph_coordinates(G: nx.Graph) -> None:
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nx.Graph: The graph with adjusted 'z' attribute for each node.
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"""
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if surface_depth >= 1.0:
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surface_depth
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# Compute subclusters as connected components
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#
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surface_depth -= 1e-6 # Cap the surface depth to prevent a value of 1.0
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# Compute subclusters as connected components
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connected_components = list(nx.connected_components(G))
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subcluster_strengths = {}
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max_strength = 0
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# Precompute strengths and track the maximum strength
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for component in connected_components:
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size = len(component)
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max_strength = max(max_strength, size)
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for node in component:
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subcluster_strengths[node] = size
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# Avoid repeated lookups and computations by pre-fetching node data
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nodes = list(G.nodes(data=True))
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node_updates = {}
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for node, attrs in nodes:
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strength = subcluster_strengths[node]
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normalized_surface_depth = (strength / max_strength) * surface_depth
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x, y, z =
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x, y, z = attrs["x"], attrs["y"], attrs["z"]
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norm = np.sqrt(x**2 + y**2 + z**2)
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adjusted_z = z - (z / norm) * normalized_surface_depth
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node_updates[node] = {"z": adjusted_z}
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# Batch update node attributes
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nx.set_node_attributes(G, node_updates)
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return G
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"""
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risk/network/graph/api
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~~~~~~~~~~~~~~~~~~~~~~
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"""
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import copy
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from typing import Any, Dict
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import networkx as nx
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import pandas as pd
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from risk.annotations import define_top_annotations
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from risk.log import logger, log_header, params
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from risk.neighborhoods import (
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define_domains,
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process_neighborhoods,
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trim_domains,
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)
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from risk.network.graph.network import NetworkGraph
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from risk.stats import calculate_significance_matrices
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class GraphAPI:
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"""Handles the loading of network graphs and associated data.
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The GraphAPI class provides methods to load and process network graphs, annotations, and neighborhoods.
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"""
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def __init__() -> None:
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pass
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def load_graph(
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self,
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network: nx.Graph,
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annotations: Dict[str, Any],
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neighborhoods: Dict[str, Any],
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tail: str = "right",
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pval_cutoff: float = 0.01,
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fdr_cutoff: float = 0.9999,
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impute_depth: int = 0,
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prune_threshold: float = 0.0,
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linkage_criterion: str = "distance",
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linkage_method: str = "average",
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linkage_metric: str = "yule",
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min_cluster_size: int = 5,
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max_cluster_size: int = 1000,
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) -> NetworkGraph:
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"""Load and process the network graph, defining top annotations and domains.
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Args:
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network (nx.Graph): The network graph.
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annotations (Dict[str, Any]): The annotations associated with the network.
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neighborhoods (Dict[str, Any]): Neighborhood significance data.
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tail (str, optional): Type of significance tail ("right", "left", "both"). Defaults to "right".
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pval_cutoff (float, optional): p-value cutoff for significance. Defaults to 0.01.
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fdr_cutoff (float, optional): FDR cutoff for significance. Defaults to 0.9999.
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impute_depth (int, optional): Depth for imputing neighbors. Defaults to 0.
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prune_threshold (float, optional): Distance threshold for pruning neighbors. Defaults to 0.0.
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linkage_criterion (str, optional): Clustering criterion for defining domains. Defaults to "distance".
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linkage_method (str, optional): Clustering method to use. Defaults to "average".
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linkage_metric (str, optional): Metric to use for calculating distances. Defaults to "yule".
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min_cluster_size (int, optional): Minimum size for clusters. Defaults to 5.
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max_cluster_size (int, optional): Maximum size for clusters. Defaults to 1000.
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Returns:
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NetworkGraph: A fully initialized and processed NetworkGraph object.
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"""
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# Log the parameters and display headers
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log_header("Finding significant neighborhoods")
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params.log_graph(
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tail=tail,
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pval_cutoff=pval_cutoff,
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fdr_cutoff=fdr_cutoff,
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impute_depth=impute_depth,
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prune_threshold=prune_threshold,
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linkage_criterion=linkage_criterion,
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linkage_method=linkage_method,
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linkage_metric=linkage_metric,
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min_cluster_size=min_cluster_size,
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max_cluster_size=max_cluster_size,
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)
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# Make a copy of the network to avoid modifying the original
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network = copy.deepcopy(network)
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logger.debug(f"p-value cutoff: {pval_cutoff}")
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logger.debug(f"FDR BH cutoff: {fdr_cutoff}")
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logger.debug(
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f"Significance tail: '{tail}' ({'enrichment' if tail == 'right' else 'depletion' if tail == 'left' else 'both'})"
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)
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# Calculate significant neighborhoods based on the provided parameters
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significant_neighborhoods = calculate_significance_matrices(
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neighborhoods["depletion_pvals"],
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neighborhoods["enrichment_pvals"],
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tail=tail,
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pval_cutoff=pval_cutoff,
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fdr_cutoff=fdr_cutoff,
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)
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log_header("Processing neighborhoods")
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# Process neighborhoods by imputing and pruning based on the given settings
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processed_neighborhoods = process_neighborhoods(
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network=network,
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neighborhoods=significant_neighborhoods,
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impute_depth=impute_depth,
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prune_threshold=prune_threshold,
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)
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log_header("Finding top annotations")
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logger.debug(f"Min cluster size: {min_cluster_size}")
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logger.debug(f"Max cluster size: {max_cluster_size}")
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# Define top annotations based on processed neighborhoods
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top_annotations = self._define_top_annotations(
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network=network,
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annotations=annotations,
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neighborhoods=processed_neighborhoods,
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min_cluster_size=min_cluster_size,
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max_cluster_size=max_cluster_size,
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)
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log_header("Optimizing distance threshold for domains")
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# Extract the significant significance matrix from the neighborhoods data
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significant_neighborhoods_significance = processed_neighborhoods[
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"significant_significance_matrix"
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]
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# Define domains in the network using the specified clustering settings
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domains = define_domains(
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top_annotations=top_annotations,
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significant_neighborhoods_significance=significant_neighborhoods_significance,
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linkage_criterion=linkage_criterion,
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linkage_method=linkage_method,
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linkage_metric=linkage_metric,
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)
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# Trim domains and top annotations based on cluster size constraints
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domains, trimmed_domains = trim_domains(
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domains=domains,
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top_annotations=top_annotations,
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min_cluster_size=min_cluster_size,
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max_cluster_size=max_cluster_size,
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)
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# Prepare node mapping and significance sums for the final NetworkGraph object
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ordered_nodes = annotations["ordered_nodes"]
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node_label_to_id = dict(zip(ordered_nodes, range(len(ordered_nodes))))
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node_significance_sums = processed_neighborhoods["node_significance_sums"]
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# Return the fully initialized NetworkGraph object
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return NetworkGraph(
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network=network,
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annotations=annotations,
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neighborhoods=neighborhoods,
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domains=domains,
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trimmed_domains=trimmed_domains,
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node_label_to_node_id_map=node_label_to_id,
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node_significance_sums=node_significance_sums,
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)
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def _define_top_annotations(
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self,
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network: nx.Graph,
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annotations: Dict[str, Any],
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neighborhoods: Dict[str, Any],
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min_cluster_size: int = 5,
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max_cluster_size: int = 1000,
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) -> pd.DataFrame:
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"""Define top annotations for the network.
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Args:
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network (nx.Graph): The network graph.
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annotations (Dict[str, Any]): Annotations data for the network.
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neighborhoods (Dict[str, Any]): Neighborhood significance data.
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min_cluster_size (int, optional): Minimum size for clusters. Defaults to 5.
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max_cluster_size (int, optional): Maximum size for clusters. Defaults to 1000.
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Returns:
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Dict[str, Any]: Top annotations identified within the network.
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"""
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# Extract necessary data from annotations and neighborhoods
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ordered_annotations = annotations["ordered_annotations"]
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neighborhood_significance_sums = neighborhoods["neighborhood_significance_counts"]
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significant_significance_matrix = neighborhoods["significant_significance_matrix"]
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significant_binary_significance_matrix = neighborhoods[
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"significant_binary_significance_matrix"
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]
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# Call external function to define top annotations
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return define_top_annotations(
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network=network,
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ordered_annotation_labels=ordered_annotations,
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neighborhood_significance_sums=neighborhood_significance_sums,
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significant_significance_matrix=significant_significance_matrix,
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significant_binary_significance_matrix=significant_binary_significance_matrix,
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min_cluster_size=min_cluster_size,
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max_cluster_size=max_cluster_size,
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)
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@@ -0,0 +1,269 @@
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"""
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risk/network/graph/network
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~~~~~~~~~~~~~~~~~~~~~~~~~~
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"""
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+
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from collections import defaultdict
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from typing import Any, Dict, List
|
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+
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import networkx as nx
|
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import numpy as np
|
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import pandas as pd
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+
|
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from risk.network.graph.summary import AnalysisSummary
|
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+
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+
|
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class NetworkGraph:
|
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"""A class to represent a network graph and process its nodes and edges.
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18
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+
|
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The NetworkGraph class provides functionality to handle and manipulate a network graph,
|
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+
including managing domains, annotations, and node significance data. It also includes methods
|
21
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+
for transforming and mapping graph coordinates, as well as generating colors based on node
|
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significance.
|
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+
"""
|
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+
|
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def __init__(
|
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self,
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network: nx.Graph,
|
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annotations: Dict[str, Any],
|
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neighborhoods: Dict[str, Any],
|
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domains: pd.DataFrame,
|
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trimmed_domains: pd.DataFrame,
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node_label_to_node_id_map: Dict[str, Any],
|
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node_significance_sums: np.ndarray,
|
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):
|
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"""Initialize the NetworkGraph object.
|
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+
|
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+
Args:
|
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+
network (nx.Graph): The network graph.
|
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+
annotations (Dict[str, Any]): The annotations associated with the network.
|
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+
neighborhoods (Dict[str, Any]): Neighborhood significance data.
|
41
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+
domains (pd.DataFrame): DataFrame containing domain data for the network nodes.
|
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+
trimmed_domains (pd.DataFrame): DataFrame containing trimmed domain data for the network nodes.
|
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|
+
node_label_to_node_id_map (Dict[str, Any]): A dictionary mapping node labels to their corresponding IDs.
|
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+
node_significance_sums (np.ndarray): Array containing the significant sums for the nodes.
|
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+
"""
|
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+
# Initialize self.network downstream of the other attributes
|
47
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+
# All public attributes can be accessed after initialization
|
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+
self.domain_id_to_node_ids_map = self._create_domain_id_to_node_ids_map(domains)
|
49
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+
self.domain_id_to_domain_terms_map = self._create_domain_id_to_domain_terms_map(
|
50
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+
trimmed_domains
|
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+
)
|
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+
self.domain_id_to_domain_info_map = self._create_domain_id_to_domain_info_map(
|
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+
trimmed_domains
|
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+
)
|
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+
self.node_id_to_domain_ids_and_significance_map = (
|
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+
self._create_node_id_to_domain_ids_and_significances(domains)
|
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+
)
|
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+
self.node_id_to_node_label_map = {v: k for k, v in node_label_to_node_id_map.items()}
|
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+
self.node_label_to_significance_map = dict(
|
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zip(node_label_to_node_id_map.keys(), node_significance_sums)
|
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+
)
|
62
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+
self.node_significance_sums = node_significance_sums
|
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+
self.node_label_to_node_id_map = node_label_to_node_id_map
|
64
|
+
|
65
|
+
# NOTE: Below this point, instance attributes (i.e., self) will be used!
|
66
|
+
self.domain_id_to_node_labels_map = self._create_domain_id_to_node_labels_map()
|
67
|
+
# Unfold the network's 3D coordinates to 2D and extract node coordinates
|
68
|
+
self.network = _unfold_sphere_to_plane(network)
|
69
|
+
self.node_coordinates = _extract_node_coordinates(self.network)
|
70
|
+
|
71
|
+
# NOTE: Only after the above attributes are initialized, we can create the summary
|
72
|
+
self.summary = AnalysisSummary(annotations, neighborhoods, self)
|
73
|
+
|
74
|
+
def pop(self, domain_id: str) -> None:
|
75
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+
"""Remove domain ID from instance domain ID mappings. This can be useful for cleaning up
|
76
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+
domain-specific mappings based on a given criterion, as domain attributes are stored and
|
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+
accessed only in dictionaries modified by this method.
|
78
|
+
|
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|
+
Args:
|
80
|
+
key (str): The domain ID key to be removed from each mapping.
|
81
|
+
"""
|
82
|
+
# Define the domain mappings to be updated
|
83
|
+
domain_mappings = [
|
84
|
+
self.domain_id_to_node_ids_map,
|
85
|
+
self.domain_id_to_domain_terms_map,
|
86
|
+
self.domain_id_to_domain_info_map,
|
87
|
+
self.domain_id_to_node_labels_map,
|
88
|
+
]
|
89
|
+
# Remove the specified domain_id key from each mapping if it exists
|
90
|
+
for mapping in domain_mappings:
|
91
|
+
if domain_id in mapping:
|
92
|
+
mapping.pop(domain_id)
|
93
|
+
|
94
|
+
# Remove the domain_id from the node_id_to_domain_ids_and_significance_map
|
95
|
+
for _, domain_info in self.node_id_to_domain_ids_and_significance_map.items():
|
96
|
+
if domain_id in domain_info["domains"]:
|
97
|
+
domain_info["domains"].remove(domain_id)
|
98
|
+
domain_info["significances"].pop(domain_id)
|
99
|
+
|
100
|
+
@staticmethod
|
101
|
+
def _create_domain_id_to_node_ids_map(domains: pd.DataFrame) -> Dict[int, Any]:
|
102
|
+
"""Create a mapping from domains to the list of node IDs belonging to each domain.
|
103
|
+
|
104
|
+
Args:
|
105
|
+
domains (pd.DataFrame): DataFrame containing domain information, including the 'primary domain' for each node.
|
106
|
+
|
107
|
+
Returns:
|
108
|
+
Dict[int, Any]: A dictionary where keys are domain IDs and values are lists of node IDs belonging to each domain.
|
109
|
+
"""
|
110
|
+
cleaned_domains_matrix = domains.reset_index()[["index", "primary_domain"]]
|
111
|
+
node_to_domains_map = cleaned_domains_matrix.set_index("index")["primary_domain"].to_dict()
|
112
|
+
domain_id_to_node_ids_map = defaultdict(list)
|
113
|
+
for k, v in node_to_domains_map.items():
|
114
|
+
domain_id_to_node_ids_map[v].append(k)
|
115
|
+
|
116
|
+
return domain_id_to_node_ids_map
|
117
|
+
|
118
|
+
@staticmethod
|
119
|
+
def _create_domain_id_to_domain_terms_map(trimmed_domains: pd.DataFrame) -> Dict[int, Any]:
|
120
|
+
"""Create a mapping from domain IDs to their corresponding terms.
|
121
|
+
|
122
|
+
Args:
|
123
|
+
trimmed_domains (pd.DataFrame): DataFrame containing domain IDs and their corresponding labels.
|
124
|
+
|
125
|
+
Returns:
|
126
|
+
Dict[int, Any]: A dictionary mapping domain IDs to their corresponding terms.
|
127
|
+
"""
|
128
|
+
return dict(
|
129
|
+
zip(
|
130
|
+
trimmed_domains.index,
|
131
|
+
trimmed_domains["normalized_description"],
|
132
|
+
)
|
133
|
+
)
|
134
|
+
|
135
|
+
@staticmethod
|
136
|
+
def _create_domain_id_to_domain_info_map(
|
137
|
+
trimmed_domains: pd.DataFrame,
|
138
|
+
) -> Dict[int, Dict[str, Any]]:
|
139
|
+
"""Create a mapping from domain IDs to their corresponding full description and significance score,
|
140
|
+
with scores sorted in descending order.
|
141
|
+
|
142
|
+
Args:
|
143
|
+
trimmed_domains (pd.DataFrame): DataFrame containing domain IDs, full descriptions, and significance scores.
|
144
|
+
|
145
|
+
Returns:
|
146
|
+
Dict[int, Dict[str, Any]]: A dictionary mapping domain IDs (int) to a dictionary with 'full_descriptions' and
|
147
|
+
'significance_scores', both sorted by significance score in descending order.
|
148
|
+
"""
|
149
|
+
# Initialize an empty dictionary to store full descriptions and significance scores of domains
|
150
|
+
domain_info_map = {}
|
151
|
+
# Domain IDs are the index of the DataFrame (it's common for some IDs to be missing)
|
152
|
+
for domain_id in trimmed_domains.index:
|
153
|
+
# Sort full_descriptions and significance_scores by significance_scores in descending order
|
154
|
+
descriptions_and_scores = sorted(
|
155
|
+
zip(
|
156
|
+
trimmed_domains.at[domain_id, "full_descriptions"],
|
157
|
+
trimmed_domains.at[domain_id, "significance_scores"],
|
158
|
+
),
|
159
|
+
key=lambda x: x[1], # Sort by significance score
|
160
|
+
reverse=True, # Descending order
|
161
|
+
)
|
162
|
+
# Unzip the sorted tuples back into separate lists
|
163
|
+
sorted_descriptions, sorted_scores = zip(*descriptions_and_scores)
|
164
|
+
# Assign to the domain info map
|
165
|
+
domain_info_map[int(domain_id)] = {
|
166
|
+
"full_descriptions": list(sorted_descriptions),
|
167
|
+
"significance_scores": list(sorted_scores),
|
168
|
+
}
|
169
|
+
|
170
|
+
return domain_info_map
|
171
|
+
|
172
|
+
@staticmethod
|
173
|
+
def _create_node_id_to_domain_ids_and_significances(domains: pd.DataFrame) -> Dict[int, Dict]:
|
174
|
+
"""Creates a dictionary mapping each node ID to its corresponding domain IDs and significance values.
|
175
|
+
|
176
|
+
Args:
|
177
|
+
domains (pd.DataFrame): A DataFrame containing domain information for each node. Assumes the last
|
178
|
+
two columns are 'all domains' and 'primary domain', which are excluded from processing.
|
179
|
+
|
180
|
+
Returns:
|
181
|
+
Dict[int, Dict]: A dictionary where the key is the node ID (index of the DataFrame), and the value is another dictionary
|
182
|
+
with 'domain' (a list of domain IDs with non-zero significance) and 'significance'
|
183
|
+
(a dict of domain IDs and their corresponding significance values).
|
184
|
+
"""
|
185
|
+
# Initialize an empty dictionary to store the result
|
186
|
+
node_id_to_domain_ids_and_significances = {}
|
187
|
+
# Get the list of domain columns (excluding 'all domains' and 'primary domain')
|
188
|
+
domain_columns = domains.columns[
|
189
|
+
:-2
|
190
|
+
] # The last two columns are 'all domains' and 'primary domain'
|
191
|
+
# Iterate over each row in the dataframe
|
192
|
+
for idx, row in domains.iterrows():
|
193
|
+
# Get the domains (column names) where the significance score is greater than 0
|
194
|
+
all_domains = domain_columns[row[domain_columns] > 0].tolist()
|
195
|
+
# Get the significance values for those domains
|
196
|
+
significance_values = row[all_domains].to_dict()
|
197
|
+
# Store the result in the dictionary with index as the key
|
198
|
+
node_id_to_domain_ids_and_significances[idx] = {
|
199
|
+
"domains": all_domains, # The column names where significance > 0
|
200
|
+
"significances": significance_values, # The actual significance values for those columns
|
201
|
+
}
|
202
|
+
|
203
|
+
return node_id_to_domain_ids_and_significances
|
204
|
+
|
205
|
+
def _create_domain_id_to_node_labels_map(self) -> Dict[int, List[str]]:
|
206
|
+
"""Create a map from domain IDs to node labels.
|
207
|
+
|
208
|
+
Returns:
|
209
|
+
Dict[int, List[str]]: A dictionary mapping domain IDs to the corresponding node labels.
|
210
|
+
"""
|
211
|
+
domain_id_to_label_map = {}
|
212
|
+
for domain_id, node_ids in self.domain_id_to_node_ids_map.items():
|
213
|
+
domain_id_to_label_map[domain_id] = [
|
214
|
+
self.node_id_to_node_label_map[node_id] for node_id in node_ids
|
215
|
+
]
|
216
|
+
|
217
|
+
return domain_id_to_label_map
|
218
|
+
|
219
|
+
|
220
|
+
def _unfold_sphere_to_plane(G: nx.Graph) -> nx.Graph:
|
221
|
+
"""Convert 3D coordinates to 2D by unfolding a sphere to a plane.
|
222
|
+
|
223
|
+
Args:
|
224
|
+
G (nx.Graph): A network graph with 3D coordinates. Each node should have 'x', 'y', and 'z' attributes.
|
225
|
+
|
226
|
+
Returns:
|
227
|
+
nx.Graph: The network graph with updated 2D coordinates (only 'x' and 'y').
|
228
|
+
"""
|
229
|
+
for node in G.nodes():
|
230
|
+
if "z" in G.nodes[node]:
|
231
|
+
# Extract 3D coordinates
|
232
|
+
x, y, z = G.nodes[node]["x"], G.nodes[node]["y"], G.nodes[node]["z"]
|
233
|
+
# Calculate spherical coordinates theta and phi from Cartesian coordinates
|
234
|
+
r = np.sqrt(x**2 + y**2 + z**2)
|
235
|
+
theta = np.arctan2(y, x)
|
236
|
+
phi = np.arccos(z / r)
|
237
|
+
|
238
|
+
# Convert spherical coordinates to 2D plane coordinates
|
239
|
+
unfolded_x = (theta + np.pi) / (2 * np.pi) # Shift and normalize theta to [0, 1]
|
240
|
+
unfolded_x = unfolded_x + 0.5 if unfolded_x < 0.5 else unfolded_x - 0.5
|
241
|
+
unfolded_y = (np.pi - phi) / np.pi # Reflect phi and normalize to [0, 1]
|
242
|
+
# Update network node attributes
|
243
|
+
G.nodes[node]["x"] = unfolded_x
|
244
|
+
G.nodes[node]["y"] = -unfolded_y
|
245
|
+
# Remove the 'z' coordinate as it's no longer needed
|
246
|
+
del G.nodes[node]["z"]
|
247
|
+
|
248
|
+
return G
|
249
|
+
|
250
|
+
|
251
|
+
def _extract_node_coordinates(G: nx.Graph) -> np.ndarray:
|
252
|
+
"""Extract 2D coordinates of nodes from the graph.
|
253
|
+
|
254
|
+
Args:
|
255
|
+
G (nx.Graph): The network graph with node coordinates.
|
256
|
+
|
257
|
+
Returns:
|
258
|
+
np.ndarray: Array of node coordinates with shape (num_nodes, 2).
|
259
|
+
"""
|
260
|
+
# Extract x and y coordinates from graph nodes
|
261
|
+
x_coords = dict(G.nodes.data("x"))
|
262
|
+
y_coords = dict(G.nodes.data("y"))
|
263
|
+
coordinates_dicts = [x_coords, y_coords]
|
264
|
+
# Combine x and y coordinates into a single array
|
265
|
+
node_positions = {
|
266
|
+
node: np.array([coords[node] for coords in coordinates_dicts]) for node in x_coords
|
267
|
+
}
|
268
|
+
node_coordinates = np.vstack(list(node_positions.values()))
|
269
|
+
return node_coordinates
|