complete review edits

d33bs · Jan 10, 2023 · 08bbb0f · 08bbb0f
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commit 08bbb0f
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Showing 12 changed files with 26 additions and 455 deletions.
diff --git a/5_analyze_data/5.analyze_data.yml b/5_analyze_data/5.analyze_data.yml
@@ -6,7 +6,6 @@ dependencies:
   - conda-forge::jupyter=1.0.0
   - conda-forge::jupyterlab
   - conda-forge::pandas=1.4.4
-  - conda-forge::plotnine
   - conda-forge::ipykernel
   - conda-forge::nb_conda_kernels
   - conda-forge::jupyter_contrib_nbextensions
@@ -16,4 +15,3 @@ dependencies:
   - conda-forge::seaborn
   - conda-forge::umap-learn
   - conda-forge::matplotlib
-
diff --git a/5_analyze_data/notebooks/UMAP_analysis/UMAPs/2D_umap_nf1_genotype.png b/5_analyze_data/notebooks/UMAP_analysis/UMAPs/2D_umap_nf1_genotype.png
diff --git a/5_analyze_data/notebooks/UMAP_analysis/UMAPs/2D_umap_nf1_num_sc.png b/5_analyze_data/notebooks/UMAP_analysis/UMAPs/2D_umap_nf1_num_sc.png
diff --git a/5_analyze_data/notebooks/UMAP_analysis/UMAPs/2D_umap_nf1_well.png b/5_analyze_data/notebooks/UMAP_analysis/UMAPs/2D_umap_nf1_well.png
diff --git a/5_analyze_data/notebooks/UMAP_analysis/UMAPs/2D_umap_nf1_well_column_num.png b/5_analyze_data/notebooks/UMAP_analysis/UMAPs/2D_umap_nf1_well_column_num.png
diff --git a/5_analyze_data/notebooks/UMAP_analysis/UMAPutils.py b/5_analyze_data/notebooks/UMAP_analysis/UMAPutils.py
@@ -1,13 +1,20 @@
+"""
+This file contains functions to assist in creating a .csv file containing 2D embeddings from 
+the NF1 normalized and feature selected morphological readouts.
+"""
+
 import pathlib
 import pandas as pd
 
 def split_data(pycytominer_output: pd.DataFrame):
     """
     split pycytominer output to metadata dataframe and np array of feature values
+
     Parameters
     ----------
     pycytominer_output : pd.DataFrame
         dataframe with pycytominer output
+
     Returns
     -------
     pd.Dataframe, np.ndarray
@@ -47,6 +54,7 @@ def merge_metadata_embeddings(
     Returns
     -------
     pd.Dataframe
+        merged dataframe with metadata and embeddings
     """
     # reset index to remove the 'Metadata_WellRow' as the index then drop the index
     metadata_dataframe = metadata_dataframe.reset_index()

diff --git a/5_analyze_data/notebooks/UMAP_analysis/add_singlecell_count_to_csv.ipynb b/5_analyze_data/notebooks/UMAP_analysis/add_singlecell_count_to_csv.ipynb
diff --git a/5_analyze_data/notebooks/UMAP_analysis/get_2D_umap_embeddings_nf1.ipynb b/5_analyze_data/notebooks/UMAP_analysis/get_2D_umap_embeddings_nf1.ipynb
@@ -24,13 +24,8 @@
    "source": [
     "import pathlib\n",
     "import pandas as pd\n",
-    "import seaborn as sns\n",
-    "from matplotlib.colors import rgb2hex\n",
-    "from mpl_toolkits.mplot3d import axes3d, Axes3D\n",
     "import umap\n",
     "\n",
-    "import sys\n",
-    "sys.path.append(\"../\")\n",
     "import UMAPutils as utils"
    ]
   },