Skip to content

Avoid 'np.float' Deprecation Error for numpy>=1.20 #21

New issue

Have a question about this project? Sign up for a free GitHub account to open an issue and contact its maintainers and the community.

Sign up for GitHub

By clicking “Sign up for GitHub”, you agree to our terms of service and privacy statement. We’ll occasionally send you account related emails.

Already on GitHub? Sign in to your account

Open
yuifu wants to merge 1 commit into
base: main
Choose a base branch
from
Open

Avoid 'np.float' Deprecation Error for numpy>=1.20 #21

Changes from all commits
Commits
Show all changes
1 commit
Select commit
File filter

Filter by extension

Filter by extension
Conversations
Failed to load comments.
Loading
Jump to
Jump to file
Failed to load files.
Loading
Diff view
Diff view
8 changes: 4 additions & 4 deletions spatialdm/utils.py
View file
Open in desktop
Original file line number Diff line number Diff line change
Expand Up @@ -175,7 +175,7 @@ def pair_selection_matrix(adata, n_perm, sel_ind, method):

# averaged ligand values
L1 = [pd.Series(x[0]).dropna().values for x in ligand.values]
L_mat = [adata[:, L1[l]].X.astype(np.float)[:, 0] for l in range(len(L1))]
L_mat = [adata[:, L1[l]].X.astype(np.float16)[:, 0] for l in range(len(L1))]
for i, k in enumerate(ligand.index):
if len(ligand.loc[k].dropna()) > 1:
if adata.uns['mean'] == 'geometric':
Expand All @@ -185,7 +185,7 @@ def pair_selection_matrix(adata, n_perm, sel_ind, method):

# averaged receptor values
R1 = [pd.Series(x[0]).dropna().values for x in receptor.values]
R_mat = [adata[:, R1[r]].X.astype(np.float)[:, 0] for r in range(len(R1))]
R_mat = [adata[:, R1[r]].X.astype(np.float16)[:, 0] for r in range(len(R1))]
for i, k in enumerate(receptor.index):
if len(receptor.loc[k].dropna()) > 1:
if adata.uns['mean'] == 'geometric':
Expand Down Expand Up @@ -248,7 +248,7 @@ def spot_selection_matrix(adata, ligand, receptor, ind, n_perm, method, scale_X=
if adata.uns['mean'] == 'geometric':
from scipy.stats.mstats import gmean
L1 = [pd.Series(x[0]).dropna().values for x in ligand.values]
L_mat0 = [raw_norm[:, L1[l]].X.A.astype(np.float)[:, 0] for l in range(len(L1))]
L_mat0 = [raw_norm[:, L1[l]].X.A.astype(np.float16)[:, 0] for l in range(len(L1))]
for i, k in enumerate(ligand.index):
if len(ligand.loc[k].dropna()) > 1:
if adata.uns['mean'] == 'geometric':
Expand All @@ -258,7 +258,7 @@ def spot_selection_matrix(adata, ligand, receptor, ind, n_perm, method, scale_X=

# averaged receptor values
R1 = [pd.Series(x[0]).dropna().values for x in receptor.values]
R_mat0 = [raw_norm[:, R1[r]].X.A.astype(np.float)[:, 0] for r in range(len(R1))]
R_mat0 = [raw_norm[:, R1[r]].X.A.astype(np.float16)[:, 0] for r in range(len(R1))]
for i, k in enumerate(receptor.index):
if len(receptor.loc[k].dropna()) > 1:
if adata.uns['mean'] == 'geometric':
Expand Down