Merge pull request #37 from YosefLab/canergen-parent

Canergen parent

popv/annotation.py

@@ -78,7 +78,7 @@ def annotate_data(
         adata.obs[["popv_prediction", "popv_prediction_score"]] = adata.obs[
             ["popv_majority_vote_prediction", "popv_majority_vote_score"]
         ]
-        adata.obs[["popv_prediction_parent"]] = adata.obs[["popv_majority_vote_prediction"]]
+        adata.obs[["popv_parent"]] = adata.obs[["popv_majority_vote_prediction"]]
     else:
         ontology_vote_onclass(adata, all_prediction_keys)
         ontology_parent_onclass(adata, all_prediction_keys)

popv/visualization.py

@@ -156,6 +156,7 @@ def prediction_score_bar_plot(
 def celltype_ratio_bar_plot(
     adata,
     popv_prediction: str | None = "popv_prediction",
+    normalize: bool = True,
     save_folder: str | None = None,
 ):
     """
@@ -167,6 +168,8 @@ def celltype_ratio_bar_plot(
         AnnData object.
     popv_prediction
         Key in adata.obs for predictions.
+    normalize
+        Plot relative cell-type abundance. Set to False to plot absolute abundance.
     save_folder
         Path to a folder for storing the plot. Defaults to None and plot is not stored.
 
@@ -182,6 +185,8 @@ def celltype_ratio_bar_plot(
     for x in cell_types:
         prop.loc[x, "query"] = np.sum(labels[is_query] == x)
         prop.loc[x, "ref"] = np.sum(labels[~is_query] == x)
+    if normalize:
+        prop = prop.div(prop.sum(axis=1))
 
     ax = prop.loc[cell_types].plot(kind="bar", figsize=(len(cell_types) * 0.5, 4), logy=True)
     ax.set_ylabel("Celltype")

pyproject.toml

@@ -33,6 +33,8 @@ dependencies = [
     "gdown>4.6.0",
     "h5py>3.7.0",
     "huggingface-hub>=0.11.1",
+    "jax<0.4.24", # Remove with scvi-tools 1.1
+    "jaxlib<0.4.24",
     "onclass>=1.3",
     "scanorama>1.7.2",
     "scanpy>1.9.0",

tests/core/test_models.py

@@ -177,7 +177,7 @@ def test_celltypist():
 def test_annotation():
     """Test Annotation and Plotting pipeline."""
     adata = _get_test_anndata().adata
-    popv.annotation.annotate_data(adata, methods=["svm", "rf"], save_path=None)
+    popv.annotation.annotate_data(adata, methods=["svm", "rf"], save_path="tests/tmp_testing/popv_test_results/")
     popv.visualization.agreement_score_bar_plot(adata)
     popv.visualization.prediction_score_bar_plot(adata)
     popv.visualization.make_agreement_plots(adata, prediction_keys=adata.uns["prediction_keys"])
@@ -190,7 +190,7 @@ def test_annotation():
 def test_annotation_no_ontology():
     """Test Annotation and Plotting pipeline without ontology."""
     adata = _get_test_anndata(cl_obo_folder=False).adata
-    popv.annotation.annotate_data(adata, methods=["svm", "rf"], save_path=None)
+    popv.annotation.annotate_data(adata, methods=["svm", "rf"], save_path="tests/tmp_testing/popv_test_results/")
     popv.visualization.agreement_score_bar_plot(adata)
     popv.visualization.prediction_score_bar_plot(adata)
     popv.visualization.make_agreement_plots(adata, prediction_keys=adata.uns["prediction_keys"])