Fix Connectivity Graph (V1)

src/bayestme/cli/load_spaceranger.py

@@ -1,9 +1,11 @@
 import argparse
 import logging
+import os.path
 
 import bayestme.common
 import bayestme.log_config
 from bayestme import data
+from bayestme.plot.common import plot_spot_connectivity_graph
 
 logger = logging.getLogger(__name__)
 
@@ -28,5 +30,12 @@ def main():
     bayestme.log_config.configure_logging(args)
 
     dataset = data.SpatialExpressionDataset.read_spaceranger(args.input)
+    plot_spot_connectivity_graph(
+        node_coordinates=dataset.positions_tissue,
+        edges=dataset.edges,
+        output_fn=os.path.join(
+            os.path.dirname(args.output), "spot_connectivity_graph.pdf"
+        ),
+    )
 
     dataset.save(args.output)

src/bayestme/data.py

@@ -33,6 +33,8 @@
 RELATIVE_EXPRESSION_ATTR = f"{BAYESTME_ANNDATA_PREFIX}_relative_expression"
 POSITIONS_X_COLUMN = "array_col"
 POSITIONS_Y_COLUMN = "array_row"
+REAL_POSITION_X_COLUMN = "pxl_col_in_fullres"
+REAL_POSITION_Y_COLUMN = "pxl_row_in_fullres"
 VISIUM_SPATIAL_COLUMNS = [
     "barcode",
     "in_tissue",
@@ -309,6 +311,13 @@ def read_spaceranger(cls, data_path):
         positions = positions_df.loc[
             ad.obs_names, [POSITIONS_X_COLUMN, POSITIONS_Y_COLUMN]
         ].values
+
+        physical_positions = positions_df.loc[
+            ad.obs_names, [REAL_POSITION_X_COLUMN, REAL_POSITION_Y_COLUMN]
+        ].values
+
+        edges = utils.get_edges(physical_positions[tissue_mask], Layout.HEX)
+
         gene_names = ad.var_names.values
         barcodes = ad.obs_names.values
         raw_count = ad.X
@@ -319,7 +328,7 @@ def read_spaceranger(cls, data_path):
             tissue_mask=tissue_mask,
             gene_names=gene_names,
             layout=Layout.HEX,
-            edges=utils.get_edges(positions[tissue_mask], Layout.HEX),
+            edges=edges,
             barcodes=barcodes,
         )
 

src/bayestme/plot/common.py

@@ -10,6 +10,7 @@
 from matplotlib.colors import Normalize
 from matplotlib.patches import RegularPolygon, Wedge, Patch, Polygon
 from scipy.spatial import Voronoi
+import networkx as nx
 
 import shapely
 from matplotlib import patches
@@ -418,3 +419,35 @@ def plot_gene_raw_counts(
 
     fig.savefig(output_file)
     plt.close(fig)
+
+
+def plot_spot_connectivity_graph(node_coordinates, edges, output_fn):
+    # Create a graph instance
+    fig, ax = plt.subplots(1, figsize=(10, 10))
+    G = nx.Graph()
+
+    # Add nodes and their positions to the graph
+    for i, (x, y) in enumerate(node_coordinates):
+        G.add_node(i, pos=(x, y))
+
+    # Add edges to the graph
+    for edge in edges:
+        G.add_edge(*edge)
+
+    # Get node positions for plotting
+    pos = nx.get_node_attributes(G, "pos")
+
+    # Draw the graph
+    nx.draw(
+        G,
+        pos,
+        with_labels=False,
+        node_color="skyblue",
+        node_size=5,
+        edge_color="gray",
+        ax=ax,
+    )
+
+    ax.set_title("Spot Connectivity Graph")
+
+    fig.savefig(output_fn)

src/bayestme/utils.py

@@ -351,22 +351,6 @@ def get_regular_grid_edges(
     return edges
 
 
-def plot_points_and_edges(positions, edges, output_path):
-    fig, ax = plt.subplots(1, 1, figsize=(10, 10))
-
-    # Plot the points
-    ax.scatter(positions[:, 0], positions[:, 1], c="blue", label="Points")
-
-    # Plot the edges
-    for edge in edges:
-        point1 = positions[edge[0], :]
-        point2 = positions[edge[1], :]
-        ax.plot([point1[0], point2[0]], [point1[1], point2[1]], c="red")
-
-    # Show the plot
-    plt.savefig(output_path, dpi=600)
-
-
 def filter_reads_to_top_n_genes(reads, n_gene):
     n_gene = min(n_gene, reads.shape[1])
     top = np.argsort(np.std(np.log(1 + reads), axis=0))[::-1]