Merge pull request #44 from jenna-tomkinson/add_main_figure_2

Add main figure 2

0.data_analysis/construct_phenotypic_expression_plate_4_fs_data/median_correlation_relationships/post_fs_aggregation_correlations/nbconverted/per_plate_correlations.py

@@ -0,0 +1,183 @@
+#!/usr/bin/env python
+# coding: utf-8
+
+# In[1]:
+
+
+import pandas as pd
+import pathlib
+import numpy as np
+
+
+# In[2]:
+
+
+# Get the current working directory
+cwd = pathlib.Path.cwd()
+
+if (cwd / ".git").is_dir():
+    root_dir = cwd
+
+else:
+    root_dir = None
+    for parent in cwd.parents:
+        if (parent / ".git").is_dir():
+            root_dir = parent
+            break
+
+# Check if a Git root directory was found
+if root_dir is None:
+    raise FileNotFoundError("No Git root directory found.")
+
+
+# ## Function for pairwise correlations
+
+# In[3]:
+
+
+def generate_correlations(df, feat_cols):
+    # Copy df so that data is not lost
+    df_corr = df.copy()
+
+    # Generate Pearson correlations between all wells
+    correlations = df_corr.loc[:, feat_cols].transpose().corr(method='pearson')
+
+    # Remove the lower triangle
+    correlations = correlations.where(np.triu(np.ones(correlations.shape), k=1).astype(bool))
+
+    # Flip, reset index, and add column names
+    correlations = correlations.stack().reset_index()
+    correlations.columns = ['group0_index', 'group1_index', 'correlation']
+
+    # Map index to corresponding Metadata_Well__group
+    correlations['Metadata_Well__group0'] = df.loc[correlations['group0_index'], 'Metadata_Well'].values
+    correlations['Metadata_Well__group1'] = df.loc[correlations['group1_index'], 'Metadata_Well'].values
+
+    correlations['Metadata_genotype__group0'] = df.loc[correlations['group0_index'], 'Metadata_genotype'].values
+    correlations['Metadata_genotype__group1'] = df.loc[correlations['group1_index'], 'Metadata_genotype'].values
+
+    # Map index to Metadata_plate
+    correlations['Metadata_plate__group0'] = df.loc[correlations['group0_index'], 'Metadata_Plate'].values
+    correlations['Metadata_plate__group1'] = df.loc[correlations['group1_index'], 'Metadata_Plate'].values
+
+    # Conditionally include Metadata_seed_density
+    if 'Metadata_seed_density' in df.columns:
+        correlations['Metadata_seed_density__group0'] = df.loc[correlations['group0_index'], 'Metadata_seed_density'].values
+        correlations['Metadata_seed_density__group1'] = df.loc[correlations['group1_index'], 'Metadata_seed_density'].values
+    else: # Default to 0 since the column has to be of the same type (can't be a str)
+        correlations['Metadata_seed_density__group0'] = 0
+        correlations['Metadata_seed_density__group1'] = 0
+
+    # Drop the index columns
+    correlations = correlations.drop(columns=['group0_index', 'group1_index'])
+
+    return correlations
+
+
+# ## Load in data and compute correlations per well
+
+# ### Plate 4 only controls
+
+# In[4]:
+
+
+# Load in plate 4 dataframe (only controls)
+plate4_path = pathlib.Path(f"{root_dir}/../nf1_cellpainting_data/3.processing_features/data/single_cell_profiles/Plate_4_bulk_camerons_method.parquet")
+plate4df = pd.read_parquet(plate4_path)
+# Fill missing values in Metadata_siRNA column with 'No Construct'
+plate4df['Metadata_siRNA'] = plate4df['Metadata_siRNA'].fillna('No Construct')
+# Only include rows where Metadata_siRNA contains 'No Construct'
+plate4df = plate4df[plate4df['Metadata_siRNA'].str.contains('No Construct')]
+
+print(plate4df.shape)
+plate4df.head()
+
+
+# ### Plate 3
+
+# In[5]:
+
+
+# Load in plate 3 dataframe
+plate3_path = pathlib.Path(f"{root_dir}/../nf1_cellpainting_data/3.processing_features/data/single_cell_profiles/Plate_3_bulk_camerons_method.parquet")
+plate3df = pd.read_parquet(plate3_path)
+
+print(plate3df.shape)
+plate3df.head()
+
+
+# ### Plate 3 prime
+
+# In[6]:
+
+
+# Load in plate 3 prime dataframe
+plate3p_path = pathlib.Path(f"{root_dir}/../nf1_cellpainting_data/3.processing_features/data/single_cell_profiles/Plate_3_prime_bulk_camerons_method.parquet")
+plate3pdf = pd.read_parquet(plate3p_path)
+
+# Update Metadata_Plate for all rows
+plate3pdf['Metadata_Plate'] = 'Plate_3_prime'
+
+print(plate3pdf.shape)
+plate3pdf.head()
+
+
+# ### Plate 5
+
+# In[7]:
+
+
+# Load in plate 3 rpime dataframe
+plate5_path = pathlib.Path(f"{root_dir}/../nf1_cellpainting_data/3.processing_features/data/single_cell_profiles/Plate_5_bulk_camerons_method.parquet")
+plate5df = pd.read_parquet(plate5_path)
+
+print(plate5df.shape)
+plate5df.head()
+
+
+# ## Concat data and generate correlations
+
+# In[8]:
+
+
+# List of dataframes
+dfs = [plate3df, plate4df, plate3pdf, plate5df]
+
+# Specified metadata columns to keep
+metadata_columns = ['Metadata_Plate', 'Metadata_Well', 'Metadata_genotype', 'Metadata_seed_density']
+
+# Find the common feature columns (not starting with 'Metadata')
+common_feature_columns = set(dfs[0].columns) - set(metadata_columns)
+for df in dfs[1:]:
+    common_feature_columns.intersection_update(set(df.columns) - set(metadata_columns))
+
+# Convert to sorted list for consistent ordering
+common_feature_columns = sorted(common_feature_columns)
+
+# Create a list of all necessary columns, metadata first
+all_columns = metadata_columns + sorted(common_feature_columns)
+
+# Reindex each dataframe to have all necessary columns, filling missing values with NaN
+dfs_reindexed = [df.reindex(columns=all_columns, fill_value=pd.NA) for df in dfs]
+
+# Concatenate the dataframes
+result = pd.concat(dfs_reindexed, ignore_index=True)
+
+print(result.shape)
+result.head()
+
+
+# In[9]:
+
+
+# Identify feature columns
+feat_cols = [col for col in result.columns if not col.startswith('Metadata')]
+
+result_corr = generate_correlations(df=result, feat_cols=feat_cols)
+
+# Save the concatenated DataFrame as a Parquet file
+result_corr.to_parquet('./construct_correlation_data/concatenated_all_plates_correlations.parquet', index=False)
+
+print(result_corr.shape)
+result_corr.head()
+