mod_docstrings8

theislab · Jan 3, 2025 · fc82248 · fc82248
1 parent d9f185a
commit fc82248
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Showing 5 changed files with 9 additions and 13 deletions.
diff --git a/docs/index.md b/docs/index.md
@@ -11,5 +11,5 @@ changelog.md
 contributing.md
 references.md
 
-notebooks/example
+notebooks/0_format_Xenium_sdata
 ```
diff --git a/docs/notebooks/0_format_Xenium_sdata.ipynb b/docs/notebooks/0_format_Xenium_sdata.ipynb
@@ -74,7 +74,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "###  Plot small region of interest"
+    "##  Plot small region of interest"
    ]
   },
   {
@@ -139,7 +139,7 @@
    "cell_type": "markdown",
    "metadata": {},
    "source": [
-    "###  Subset data to small region of interest"
+    "##  Subset data to small region of interest"
    ]
   },
   {

diff --git a/src/troutpy/tl/NMF.py b/src/troutpy/tl/NMF.py
@@ -9,8 +9,10 @@
 import matplotlib.pyplot as plt
 import numpy as np
 import seaborn as sns
+from spatialdata import SpatialData
 
-def apply_nmf_to_adata(adata, n_components=20, subsample_percentage=1.0, save=False, output_path: str = '', random_state=None):
+
+def apply_nmf_to_adata(adata:SpatialData, n_components=20, subsample_percentage=1.0, save=False, output_path: str = '', random_state=None):
     """
     Applies Non-Negative Matrix Factorization (NMF) to an AnnData object to reduce the dimensionality of gene expression data.
 
@@ -55,7 +57,7 @@ def apply_nmf_to_adata(adata, n_components=20, subsample_percentage=1.0, save=Fa
 
 
 def nmf(
-    sdata, layer='extracellular_transcripts_enriched', 
+    sdata:SpatialData, layer='extracellular_transcripts_enriched', 
     feature_key='feature_name', bin_key='bin_id', 
     density_table_key='segmentation_free_table', 
     n_components=20, subsample_percentage=0.1,

diff --git a/src/troutpy/tl/estimate_density.py b/src/troutpy/tl/estimate_density.py
@@ -1,9 +1,10 @@
 import os
 import numpy as np
 import pandas as pd
+from spatialdata import SpatialData
 
 def colocalization_proportion(
-    sdata, 
+    sdata:SpatialData, 
     outpath, 
     threshold_colocalized=1, 
     filename='proportion_of_grouped_exRNA.parquet', save=True

diff --git a/src/troutpy/tl/target_cell.py b/src/troutpy/tl/target_cell.py
@@ -4,15 +4,8 @@
 import scanpy as sc
 import seaborn as sns
 import matplotlib.pyplot as plt
-from tqdm import tqdm
-import spatialdata as sd
-
-
-
 from typing import Optional
-import numpy as np
 from tqdm import tqdm
-import scanpy as sc
 import spatialdata as sd
 from spatialdata import SpatialData