feature: shortest path finding

Author: duypham2108

stlearn/spatials/trajectory/__init__.py

@@ -11,3 +11,4 @@
 from .compare_transitions import compare_transitions
 
 from .set_root import set_root
+from .shortest_path_spatial_PAGA import shortest_path_spatial_PAGA

stlearn/spatials/trajectory/pseudotime.py

@@ -244,9 +244,8 @@ def store_available_paths(adata, threshold, use_label, max_nodes, pseudotime_key
             paths = nx.all_simple_paths(H, source=source, target=target)
             for i, path in enumerate(paths):
                 if len(path) < max_nodes:
-                    all_paths[i] = path
+                    all_paths[str(i) + "_" + str(source) + "_" + str(target)] = path
 
-    # all_paths = list(map(lambda x: " - ".join(np.array(x).astype(str)),all_paths))
 
     adata.uns["available_paths"] = all_paths
     print(

stlearn/spatials/trajectory/shortest_path_spatial_PAGA.py

@@ -0,0 +1,94 @@
+import networkx as nx
+import numpy as np
+from stlearn.utils import _read_graph
+
+def shortest_path_spatial_PAGA(adata,use_label,key="dpt_pseudotime",):
+    # Read original PAGA graph
+    G = nx.from_numpy_array(adata.uns["paga"]["connectivities"].toarray())
+    edge_weights = nx.get_edge_attributes(G, "weight")
+    G.remove_edges_from((e for e, w in edge_weights.items() if w <0))
+    H = G.to_directed()
+    
+    # Get min_node and max_node
+    min_node,max_node = find_min_max_node(adata,key,use_label)
+    
+    # Calculate pseudotime for each node
+    node_pseudotime = {}
+
+    for node in H.nodes:
+        node_pseudotime[node] = adata.obs.query(use_label + " == '" + str(node) + "'")[
+            key
+        ].max()
+
+    # Force original PAGA to directed PAGA based on pseudotime
+    edge_to_remove = []
+    for edge in H.edges:
+        if node_pseudotime[edge[0]] - node_pseudotime[edge[1]] > 0:
+            edge_to_remove.append(edge)
+    H.remove_edges_from(edge_to_remove)
+    
+    # Extract all available paths
+    all_paths = {}
+    j = 0
+    for source in H.nodes:
+        for target in H.nodes:
+            paths = nx.all_simple_paths(H, source=source, target=target)
+            for i, path in enumerate(paths):
+                j+=1
+                all_paths[j] = path
+    
+    # Filter the target paths from min_node to max_node
+    target_paths = []
+    for path in list(all_paths.values()):
+        if path[0] == min_node and path[-1] == max_node:
+            target_paths.append(path)
+    
+    # Get the global graph
+    G = _read_graph(adata, "global_graph")
+    
+    centroid_dict = adata.uns["centroid_dict"]
+    centroid_dict = {int(key): centroid_dict[key] for key in centroid_dict}
+    
+    # Generate total length of every path. Store by dictionary
+    dist_dict = {}
+    for path in target_paths:
+        path_name = ",".join(list(map(str,path)))  
+        result = []
+        query_node = get_node(path, adata.uns["split_node"])
+        for edge in G.edges():
+            if (edge[0] in query_node) and (edge[1] in query_node):
+                result.append(edge)
+        if len(result) >= len(path):
+            dist_dict[path_name] = calculate_total_dist(result,centroid_dict)
+    
+    # Find the shortest path
+    shortest_path = min(dist_dict, key=lambda x: dist_dict[x])
+    return shortest_path.split(',')
+
+# get name of cluster by subcluster
+def get_cluster(search, dictionary):
+    for cl, sub in dictionary.items():
+        if search in sub:
+            return cl
+
+def get_node(node_list, split_node):
+    result = np.array([])
+    for node in node_list:
+        result = np.append(result, np.array(split_node[int(node)]).astype(int))
+    return result.astype(int)
+
+def find_min_max_node(adata,key="dpt_pseudotime",use_label="leiden"):
+    min_cluster = int(adata.obs[adata.obs[key]==0][use_label].values[0])
+    max_cluster = int(adata.obs[adata.obs[key]==1][use_label].values[0])
+    
+    return [min_cluster,max_cluster]
+
+def calculate_total_dist(result,centroid_dict):
+    import math
+    total_dist = 0
+    for edge in result:
+        source = centroid_dict[edge[0]]
+        target = centroid_dict[edge[1]]
+        dist =math.dist(source,target)
+        total_dist += dist
+    return total_dist