UMAP notebooks and visualizations

d33bs · Jan 9, 2023 · 74d1917 · 74d1917
1 parent 9adc2b4
commit 74d1917
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Showing 30 changed files with 1,839 additions and 3,264 deletions.
diff --git a/.gitignore b/.gitignore
@@ -31,5 +31,8 @@ __pycache__/
 NF1_test
 NF1_Second_Plate_Old
 
-# Ignore test notebooks
+# ignore test notebooks
 example_code.ipynb
+
+# ignore deprecated notebooks
+5_analyze_data/notebooks/UMAP_analysis/deprecated_notebooks
diff --git a/4_processing_features/data/nf1_sc_cellprofiler.csv.gz b/4_processing_features/data/nf1_sc_cellprofiler.csv.gz
diff --git a/4_processing_features/data/nf1_sc_norm_cellprofiler.csv.gz b/4_processing_features/data/nf1_sc_norm_cellprofiler.csv.gz
diff --git a/4_processing_features/data/nf1_sc_norm_fs_cellprofiler.csv.gz b/4_processing_features/data/nf1_sc_norm_fs_cellprofiler.csv.gz
diff --git a/4_processing_features/extract_single_cell_features.ipynb b/4_processing_features/extract_single_cell_features.ipynb
@@ -827,11 +827,12 @@
    ]
   },
   {
+   "attachments": {},
    "cell_type": "markdown",
    "id": "bba06013",
    "metadata": {},
    "source": [
-    "## Feeature Selection"
+    "## Feature Selection"
    ]
   },
   {
@@ -1293,7 +1294,7 @@
    "name": "python",
    "nbconvert_exporter": "python",
    "pygments_lexer": "ipython3",
-   "version": "3.8.13 | packaged by conda-forge | (default, Mar 25 2022, 06:04:10) \n[GCC 10.3.0]"
+   "version": "3.8.13"
   },
   "vscode": {
    "interpreter": {

diff --git a/4_processing_features/extract_single_cell_features.py b/4_processing_features/extract_single_cell_features.py
@@ -116,7 +116,7 @@
 normalize_sc_df.head()
 
 
-# ## Feeature Selection
+# ## Feature Selection
 
 # In[8]:
 

diff --git a/5_analyze_data/UMAPS/norm_nf1_1D_umap.png b/5_analyze_data/UMAPS/norm_nf1_1D_umap.png
diff --git a/5_analyze_data/UMAPS/norm_nf1_2D_umap.png b/5_analyze_data/UMAPS/norm_nf1_2D_umap.png
diff --git a/5_analyze_data/UMAPS/norm_nf1_3D_umap.png b/5_analyze_data/UMAPS/norm_nf1_3D_umap.png