Daniel strobl hvg conservation fix (#785)

* hvg conservation metric fix

* pre-commit

* Allow for uppercase repo owner

* Fix sklearn req

* bash not sh

* bugfix use index

* add to api

* pre-commit

* list instead of index

* check number of genes

* pre-commit

* addressing comments

* pre-commit

* shorten line

* addressing comments

* pre-commit

* fix checks

* remove magic numbers

* pre-commit

* int -> numbers.Integral

* Fix typo

* fix dataset size assumption and duck-type hvg_unint

---------

Co-authored-by: github-actions[bot] <41898282+github-actions[bot]@users.noreply.github.com>
Co-authored-by: Scott Gigante <[email protected]>
Co-authored-by: Scott Gigante <[email protected]>
Former-commit-id: 814fedc

Author: 3 people

openproblems/tasks/_batch_integration/_common/api.py

@@ -1,10 +1,13 @@
 from ....data.sample import load_sample_data
 from ....tools.decorators import dataset
 from .utils import filter_celltypes
+from .utils import precompute_hvg
 
+import numbers
 import numpy as np
 
 MIN_CELLS_PER_CELLTYPE = 50
+N_HVG_UNINT = 2000
 
 
 def check_neighbors(adata, neighbors_key, connectivities_key, distances_key):
@@ -15,7 +18,12 @@ def check_neighbors(adata, neighbors_key, connectivities_key, distances_key):
     assert distances_key in adata.obsp
 
 
-def check_dataset(adata, do_check_pca=False, do_check_neighbors=False):
+def check_dataset(
+    adata,
+    do_check_pca=False,
+    do_check_neighbors=False,
+    do_check_hvg=False,
+):
     """Check that dataset output fits expected API."""
 
     assert "batch" in adata.obs
@@ -28,12 +36,21 @@ def check_dataset(adata, do_check_pca=False, do_check_neighbors=False):
     assert adata.var_names.is_unique
     assert adata.obs_names.is_unique
 
+    assert "n_genes_pre" in adata.uns
+    assert isinstance(adata.uns["n_genes_pre"], numbers.Integral)
+    assert adata.uns["n_genes_pre"] == adata.n_vars
+
     assert "organism" in adata.uns
     assert adata.uns["organism"] in ["mouse", "human"]
 
     if do_check_pca:
         assert "X_uni_pca" in adata.obsm
 
+    if do_check_hvg:
+        assert "hvg_unint" in adata.uns
+        assert len(adata.uns["hvg_unint"]) == min(N_HVG_UNINT, adata.n_vars)
+        assert np.all(np.isin(adata.uns["hvg_unint"], adata.var.index))
+
     if do_check_neighbors:
         check_neighbors(adata, "uni", "uni_connectivities", "uni_distances")
 
@@ -58,6 +75,10 @@ def sample_dataset(run_pca: bool = False, run_neighbors: bool = False):
     adata.obs["batch"] = np.random.choice(2, adata.shape[0], replace=True).astype(str)
     adata.obs["labels"] = np.random.choice(3, adata.shape[0], replace=True).astype(str)
     adata = filter_celltypes(adata)
+
+    adata.uns["hvg_unint"] = precompute_hvg(adata)
+    adata.uns["n_genes_pre"] = adata.n_vars
+
     if run_pca:
         adata.obsm["X_uni_pca"] = sc.pp.pca(adata.X)
     if run_neighbors:

openproblems/tasks/_batch_integration/_common/datasets/immune.py

@@ -1,6 +1,7 @@
 from .....data.immune_cells import load_immune
 from .....tools.decorators import dataset
 from ..utils import filter_celltypes
+from ..utils import precompute_hvg
 from typing import Optional
 
 
@@ -13,7 +14,11 @@
     "Smart-seq2).",
     image="openproblems",
 )
-def immune_batch(test: bool = False, min_celltype_count: Optional[int] = None):
+def immune_batch(
+    test: bool = False,
+    min_celltype_count: Optional[int] = None,
+    n_hvg: Optional[int] = None,
+):
     import scanpy as sc
 
     adata = load_immune(test)
@@ -38,4 +43,7 @@ def immune_batch(test: bool = False, min_celltype_count: Optional[int] = None):
 
     sc.pp.neighbors(adata, use_rep="X_uni_pca", key_added="uni")
     adata.var_names_make_unique()
+
+    adata.uns["hvg_unint"] = precompute_hvg(adata, n_genes=n_hvg)
+    adata.uns["n_genes_pre"] = adata.n_vars
     return adata

openproblems/tasks/_batch_integration/_common/datasets/pancreas.py

@@ -1,6 +1,7 @@
 from .....data.pancreas import load_pancreas
 from .....tools.decorators import dataset
 from ..utils import filter_celltypes
+from ..utils import precompute_hvg
 from typing import Optional
 
 
@@ -13,7 +14,11 @@
     "and SMARTER-seq).",
     image="openproblems",
 )
-def pancreas_batch(test: bool = False, min_celltype_count: Optional[int] = None):
+def pancreas_batch(
+    test: bool = False,
+    min_celltype_count: Optional[int] = None,
+    n_hvg: Optional[int] = None,
+):
     import scanpy as sc
 
     adata = load_pancreas(test)
@@ -38,4 +43,7 @@ def pancreas_batch(test: bool = False, min_celltype_count: Optional[int] = None)
     sc.pp.neighbors(adata, use_rep="X_uni_pca", key_added="uni")
 
     adata.var_names_make_unique()
+
+    adata.uns["hvg_unint"] = precompute_hvg(adata, n_genes=n_hvg)
+    adata.uns["n_genes_pre"] = adata.n_vars
     return adata

openproblems/tasks/_batch_integration/_common/utils.py

@@ -1,11 +1,27 @@
+from . import api
+from scanpy.pp import highly_variable_genes
 from typing import Optional
 
 
 def filter_celltypes(adata, min_celltype_count: Optional[int] = None):
 
-    min_celltype_count = min_celltype_count or 50
+    min_celltype_count = min_celltype_count or api.MIN_CELLS_PER_CELLTYPE
 
     celltype_counts = adata.obs["labels"].value_counts()
     keep_celltypes = celltype_counts[celltype_counts >= min_celltype_count].index
     keep_cells = adata.obs["labels"].isin(keep_celltypes)
     return adata[keep_cells].copy()
+
+
+def precompute_hvg(adata, n_genes: Optional[int] = None):
+
+    n_genes = n_genes or api.N_HVG_UNINT
+    hvg_unint = highly_variable_genes(
+        adata,
+        n_top_genes=n_genes,
+        layer="log_normalized",
+        flavor="cell_ranger",
+        batch_key="batch",
+        inplace=False,
+    )
+    return list(hvg_unint[hvg_unint.highly_variable].index)

openproblems/tasks/_batch_integration/batch_integration_feature/README.md

@@ -46,8 +46,12 @@ Datasets should contain the following attributes:
 * `adata.layers['counts']` with raw, integer UMI count data,
 * `adata.layers['log_normalized']` with log-normalized data and
 * `adata.X` with log-normalized data
+* `adata.uns['n_genes_pre']` with the number of genes present before integration
+* `adata.uns['hvg_unint']` with a list of 2000 highly variable genes
+   prior to integration (for the hvg conservation metric)
 
 Methods should store their a batch-corrected gene expression matrix in `adata.X`.
+The output should should contain at least 2000 features.
 
 The `openproblems-python-batch-integration` docker container is used for the methods
 that

openproblems/tasks/_batch_integration/batch_integration_feature/api.py

@@ -3,12 +3,19 @@
 
 import functools
 
-check_dataset = functools.partial(api.check_dataset, do_check_pca=True)
+check_dataset = functools.partial(
+    api.check_dataset, do_check_hvg=True, do_check_pca=True
+)
 
 
 def check_method(adata, is_baseline=False):
     """Check that method output fits expected API."""
     assert "log_normalized" in adata.layers
+    # check hvg_unint is still there
+    assert "hvg_unint" in adata.uns
+    # check n_vars is not too small
+    assert "n_genes_pre" in adata.uns
+    assert adata.n_vars >= min(api.N_HVG_UNINT, adata.uns["n_genes_pre"])
     if not is_baseline:
         assert adata.layers["log_normalized"] is not adata.X
     return True

openproblems/tasks/_batch_integration/batch_integration_feature/metrics/hvg_conservation.py

@@ -29,5 +29,6 @@ def hvg_conservation(adata):
 
     adata_unint = adata.copy()
     adata_unint.X = adata_unint.layers["log_normalized"]
+    hvg_both = list(set(adata.uns["hvg_unint"]).intersection(adata.var_names))
 
-    return hvg_overlap(adata_unint, adata, "batch")
+    return hvg_overlap(adata_unint, adata[:, hvg_both], "batch")