avoid depreication

dpeerlab · Apr 22, 2024 · b99f4ca · b99f4ca
1 parent 3203a45
commit b99f4ca
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Showing 2 changed files with 6 additions and 3 deletions.
diff --git a/src/palantir/io.py b/src/palantir/io.py
@@ -71,7 +71,7 @@ def from_10x(data_dir, use_ensemble_id=True):
 
 
 def from_10x_HDF5(filename, genome=None):
-    ad = sc.read_10x_h5(filename, genome, True)
+    ad = sc.read_10x_h5(filename, genome=genome, gex_only=True)
 
     dataMatrix = pd.DataFrame(ad.X.todense(), columns=ad.var_names, index=ad.obs_names)
 

diff --git a/src/palantir/utils.py b/src/palantir/utils.py
@@ -63,15 +63,18 @@ def run_pca(
         n_comps = n_components
     else:
         l_n_comps = min(1000, ad.n_obs - 1, ad.n_vars - 1)
-        sc.pp.pca(ad, n_comps=l_n_comps, use_highly_variable=True, zero_center=False)
+        sc.pp.pca(ad, n_comps=l_n_comps, mask_var="highly_variable", zero_center=False)
         try:
             n_comps = np.where(np.cumsum(ad.uns["pca"]["variance_ratio"]) > 0.85)[0][0]
         except IndexError:
             n_comps = n_components
 
     # Rerun with selection number of components
     n_comps = min(n_comps, ad.n_obs - 1, ad.n_vars - 1)
-    sc.pp.pca(ad, n_comps=n_comps, use_highly_variable=use_hvg, zero_center=False)
+    kwargs = dict()
+    if use_hvg:
+        kwargs["mask_var"] = "highly_variable"
+    sc.pp.pca(ad, n_comps=n_comps, zero_center=False, **kwargs)
 
     if isinstance(data, sc.AnnData):
         data.obsm[pca_key] = ad.obsm["X_pca"]