Better error message when there are fewer nodes than the number of dimensions in pmds layout

CHANGELOG.md

@@ -17,8 +17,8 @@ and this project adheres to [Semantic Versioning](https://semver.org/spec/v2.0.0
 
 ### Added
 
-_   Add `depth` column to `discarded_edgelist.parquet` output of the GRAPH stage that indicates at which refinement iteration the edge is removed.
-_   Add `edges_removed_in_multiplet_recovery_first_iteration`, `edges_removed_in_multiplet_recovery_refinement` and `fraction_edges_removed_in_refinement` to graph report.json.
+-   Add `depth` column to `discarded_edgelist.parquet` output of the GRAPH stage that indicates at which refinement iteration the edge is removed.
+-   Add `edges_removed_in_multiplet_recovery_first_iteration`, `edges_removed_in_multiplet_recovery_refinement` and `fraction_edges_removed_in_refinement` to graph report.json.
 -   Add `is_potential_doublet` and `n_edges_to_split_doublet` columns to adata.obs.
 -   Add `fraction_potential_doublets` and `n_edges_to_split_potential_doublets` to annotate report.json.
 -   Add `--max-edges-to-split` option to `graph` to specify the maximum number of edges that can be removed between two sub-components during multiplet recovery.
@@ -30,6 +30,11 @@ _   Add `edges_removed_in_multiplet_recovery_first_iteration`, `edges_removed_in
 
 -   Remove the `components_recovered.csv` output from the GRAPH stage.
 
+
+### Fixed
+
+- better error message when the number of nodes is lower than the number of requested dimensions in `pmds_layout`.
+
 ## [0.18.3] - 2024-09-26
 
 ### Fixed

src/pixelator/graph/backends/implementations/_networkx.py

@@ -788,8 +788,9 @@ def pmds_layout(
     if not nx.is_connected(g):
         raise ValueError("Only connected graphs are supported.")
 
-    if pivots >= len(g.nodes):
-        total_nodes = len(g.nodes)
+    n_nodes = len(g.nodes)
+    if pivots >= n_nodes:
+        total_nodes = n_nodes
         warnings.warn(
             f"'pivots' ({pivots}) should be less than the number of "
             f"nodes ({total_nodes}) in the graph. Using all nodes as 'pivots'."
@@ -802,6 +803,11 @@ def pmds_layout(
     if pivots < dim:
         raise ValueError("'pivots' must be greater than or equal to dim.")
 
+    if n_nodes <= dim:
+        raise ValueError(
+            f"Number of nodes in the graph ({n_nodes}) must be greater than or equal to 'dim' ({dim})."
+        )
+
     pivot_lower_bound = np.min([np.floor(0.2 * len(g.nodes)), 50])
     if pivots < pivot_lower_bound:
         raise ValueError(
@@ -862,6 +868,7 @@ def pmds_layout(
     # Compute SVD and use distances to compute coordinates for all nodes
     # in an abstract cartesian space
     _, _, Vh = sp.sparse.linalg.svds(D_pivs_centered, k=dim, random_state=seed)
+
     coordinates = D_pivs_centered @ np.transpose(Vh)
     # Flip the coordinates here to make sure that we get the correct coordinate ordering
     # i.e. iqr(x) > iqr(y) > iqr(z)

tests/pixeldataset/test_precomputed_layouts.py

@@ -9,6 +9,7 @@
 import pytest
 from pandas.testing import assert_frame_equal
 
+from pixelator.pixeldataset import PixelDataset
 from pixelator.pixeldataset.precomputed_layouts import (
     PreComputedLayouts,
     aggregate_precomputed_layouts,
@@ -526,6 +527,46 @@ def test_generate_precomputed_layouts_for_components_with_single_layout_algorith
         df = precomputed_layouts.to_df()
         assert set(df["layout"]) == {"pmds_3d"}
 
+    @pytest.mark.test_this
+    def test_generate_precomputed_layouts_on_to_small_components(self):
+        edgelist = pd.DataFrame.from_dict(
+            {
+                "upia": ["A", "B", "C"],
+                "upib": ["B", "C", "A"],
+                "umi": ["G", "H", "I"],
+                "sequence": ["J", "K", "L"],
+                "component": [
+                    "2ac2ca983a4b82dd",
+                    "2ac2ca983a4b82dd",
+                    "2ac2ca983a4b82dd",
+                ],
+                "marker": ["CD3", "CD3", "CD3"],
+                "count": [1, 1, 1],
+            }
+        )
+
+        class MockAnnData:
+            def __init__(self):
+                self.n_obs = 10
+
+            def copy(self):
+                return self
+
+            @property
+            def obs(self):
+                return pd.DataFrame(index=edgelist["component"].unique())
+
+            @property
+            def var(self):
+                return pd.DataFrame(index=edgelist["marker"].unique())
+
+        pixel_dataset = PixelDataset.from_data(MockAnnData(), edgelist=edgelist)
+        layout_algorithm = "wpmds_3d"
+        with pytest.raises(ValueError):
+            generate_precomputed_layouts_for_components(
+                pixel_dataset, layout_algorithms=layout_algorithm
+            )
+
 
 @pytest.mark.integration_test
 class TestGeneratePrecomputedLayoutsForComponentsIntegrationTest: