round restored counts in some affected datasets

theislab · Dec 21, 2023 · 5fcf932 · 5fcf932
1 parent 0c2f42e
commit 5fcf932
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Showing 7 changed files with 8 additions and 6 deletions.
diff --git a/...rs/loaders/d10_1016_j_cell_2020_08_001/homosapiens_blood_2020_na_schulteschrepping_001.py b/...rs/loaders/d10_1016_j_cell_2020_08_001/homosapiens_blood_2020_na_schulteschrepping_001.py
@@ -1,11 +1,13 @@
 import anndata
 import os
 import scipy.sparse
+import numpy as np
 
 
 def load(data_dir, sample_fn, **kwargs):
     fn = os.path.join(data_dir, sample_fn)
     adata = anndata.read_h5ad(fn)
+    adata.X = np.round((np.expm1(adata.X.A) * adata.obs["nCount_RNA"][:, None] / 10000))
     adata.X = scipy.sparse.csr_matrix(adata.X)
 
     return adata
diff --git a/...aloaders/loaders/d10_1016_j_devcel_2020_01_033/homosapiens_lung_2020_10x3v2_miller_001.py b/...aloaders/loaders/d10_1016_j_devcel_2020_01_033/homosapiens_lung_2020_10x3v2_miller_001.py
@@ -9,5 +9,6 @@ def load(data_dir, **kwargs):
     adata = anndata.read_h5ad(fn)
     adata.X = np.expm1(adata.X)
     adata.X = adata.X.multiply(scipy.sparse.csc_matrix(adata.obs["nUMI"].values[:, None])).multiply(1 / 10000)
+    adata.X = np.round(adata.X)
 
     return adata
diff --git a/.../dataloaders/loaders/d10_1038_s41422_018_0099_2/homosapiens_testis_2018_10x3v2_guo_001.py b/.../dataloaders/loaders/d10_1038_s41422_018_0099_2/homosapiens_testis_2018_10x3v2_guo_001.py
@@ -9,5 +9,6 @@ def load(data_dir, **kwargs):
     adata = anndata.read_h5ad(fn)
     adata.X = np.expm1(adata.X)
     adata.X = adata.X.multiply(scipy.sparse.csc_matrix(adata.obs["n_counts"].values[:, None])).multiply(1 / 10000)
+    adata.X + np.round(adata.X)
 
     return adata
diff --git a/...a/dataloaders/loaders/d10_1038_s41467_020_16066_2/homosapiens_x_2020_10x3v2_cook_001.yaml b/...a/dataloaders/loaders/d10_1038_s41467_020_16066_2/homosapiens_x_2020_10x3v2_cook_001.yaml
@@ -188,7 +188,7 @@ dataset_or_observation_wise:
     gm_obs_key:
     individual:
     individual_obs_key: 
-    organ: 
+    organ: "cell in vitro"
     organ_obs_key: 
     organism: "Homo sapiens"
     organism_obs_key: 

diff --git a/...loaders/loaders/d10_1038_s41588_019_0489_5/homosapiens_x_2019_x_mcfalinefigueroa_001.yaml b/...loaders/loaders/d10_1038_s41588_019_0489_5/homosapiens_x_2019_x_mcfalinefigueroa_001.yaml
@@ -61,7 +61,7 @@ dataset_or_observation_wise:
     gm_obs_key:
     individual:
     individual_obs_key: 
-    organ: 
+    organ: "cell in vitro"
     organ_obs_key: 
     organism: "Homo sapiens"
     organism_obs_key: 

diff --git a/...dataloaders/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001.yaml b/...dataloaders/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001.yaml
@@ -25,7 +25,7 @@ dataset_or_feature_wise:
     feature_type_var_key: 
 dataset_or_observation_wise:
     assay_sc: "10x 3' v3"
-    assay_sc_obs_key: "assay"
+    assay_sc_obs_key: 
     assay_differentiation: 
     assay_differentiation_obs_key: 
     assay_type_differentiation: 
@@ -46,7 +46,7 @@ dataset_or_observation_wise:
     gm_obs_key:
     individual:
     individual_obs_key: "Donor_Study_ID"
-    organ: 
+    organ: colon
     organ_obs_key: 
     organism: "Homo sapiens"
     organism_obs_key: 

diff --git a/...ers/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001_assay_sc.tsv b/...ers/loaders/d10_1038_s41588_022_01088_x/homosapiens_x_2022_10x3v3_becker_001_assay_sc.tsv