fuson_plm/data/split_vis.py

import matplotlib.pyplot as plt
import numpy as np
from scipy.stats import entropy
from sklearn.manifold import TSNE
import pickle
import pandas as pd
import os
from fuson_plm.utils.logging import log_update
from fuson_plm.utils.visualizing import set_font

def calculate_aa_composition(sequences):
    composition = {}
    total_length = sum([len(seq) for seq in sequences])
    
    for seq in sequences:
        for aa in seq:
            if aa in composition:
                composition[aa] += 1
            else:
                composition[aa] = 1
    
    # Convert counts to relative frequency
    for aa in composition:
        composition[aa] /= total_length
    
    return composition

def calculate_shannon_entropy(sequence):
    """
    Calculate the Shannon entropy for a given sequence.

    Args:
        sequence (str): A sequence of characters (e.g., amino acids or nucleotides).

    Returns:
        float: Shannon entropy value.
    """
    bases = set(sequence)
    counts = [sequence.count(base) for base in bases]
    return entropy(counts, base=2)

def visualize_splits_hist(train_lengths, val_lengths, test_lengths, colormap, savepath=f'../data/splits/length_distributions.png', axes=None):
    log_update('\nMaking histogram of length distributions')
    # Create a figure and axes with 1 row and 3 columns
    if axes is None:
        fig, axes = plt.subplots(1, 3, figsize=(18, 6))
    
    # Unpack the labels and titles
    xlabel, ylabel = ['Sequence Length (AA)', 'Frequency']

    # Plot the first histogram
    axes[0].hist(train_lengths, bins=20, edgecolor='k',color=colormap['train'])
    axes[0].set_xlabel(xlabel, fontsize=24)
    axes[0].set_ylabel(ylabel, fontsize=24)
    axes[0].set_title(f'Train Set Length Distribution (n={len(train_lengths)})', fontsize=24)
    axes[0].grid(True)
    axes[0].set_axisbelow(True)
    axes[0].tick_params(axis='x', labelsize=24)  # Customize x-axis tick label size
    axes[0].tick_params(axis='y', labelsize=24)  # Customize y-axis tick label size


    # Plot the second histogram
    axes[1].hist(val_lengths, bins=20, edgecolor='k',color=colormap['val'])
    axes[1].set_xlabel(xlabel, fontsize=24)
    axes[1].set_ylabel(ylabel, fontsize=24)
    axes[1].set_title(f'Validation Set Length Distribution (n={len(val_lengths)})', fontsize=24)
    axes[1].grid(True)
    axes[1].set_axisbelow(True)
    axes[1].tick_params(axis='x', labelsize=24)
    axes[1].tick_params(axis='y', labelsize=24) 

    # Plot the third histogram
    axes[2].hist(test_lengths, bins=20, edgecolor='k',color=colormap['test'])
    axes[2].set_xlabel(xlabel, fontsize=24)
    axes[2].set_ylabel(ylabel, fontsize=24)
    axes[2].set_title(f'Test Set Length Distribution (n={len(test_lengths)})', fontsize=24)
    axes[2].grid(True)
    axes[2].set_axisbelow(True)
    axes[2].tick_params(axis='x', labelsize=24)
    axes[2].tick_params(axis='y', labelsize=24) 

    # Adjust layout
    if savepath is not None:
        plt.tight_layout()

        # Save the figure
        plt.savefig(savepath)
    
def visualize_splits_scatter(train_clusters, val_clusters, test_clusters, benchmark_cluster_reps, colormap, savepath='../data/splits/scatterplot.png', ax=None):
    log_update("\nMaking scatterplot with distribution of cluster sizes across train, test, and val")
    # Make grouped versions of these DataFrames for size analysis
    train_clustersgb = train_clusters.groupby('representative seq_id')['member seq_id'].count().reset_index().rename(columns={'member seq_id':'member count'})
    val_clustersgb = val_clusters.groupby('representative seq_id')['member seq_id'].count().reset_index().rename(columns={'member seq_id':'member count'})
    test_clustersgb = test_clusters.groupby('representative seq_id')['member seq_id'].count().reset_index().rename(columns={'member seq_id':'member count'})
    
    # Isolate benchmark-containing clusters so their contribution can be plotted separately
    total_test_proteins = sum(test_clustersgb['member count'])
    test_clustersgb['benchmark cluster'] = test_clustersgb['representative seq_id'].isin(benchmark_cluster_reps)
    benchmark_clustersgb = test_clustersgb.loc[test_clustersgb['benchmark cluster']].reset_index(drop=True)
    test_clustersgb = test_clustersgb.loc[test_clustersgb['benchmark cluster']==False].reset_index(drop=True)
    
    # Convert them to value counts
    train_clustersgb = train_clustersgb['member count'].value_counts().reset_index().rename(columns={'index':'cluster size (n_members)','member count': 'n_clusters'})
    val_clustersgb = val_clustersgb['member count'].value_counts().reset_index().rename(columns={'index':'cluster size (n_members)','member count': 'n_clusters'})
    test_clustersgb = test_clustersgb['member count'].value_counts().reset_index().rename(columns={'index':'cluster size (n_members)','member count': 'n_clusters'})
    benchmark_clustersgb = benchmark_clustersgb['member count'].value_counts().reset_index().rename(columns={'index':'cluster size (n_members)','member count': 'n_clusters'})
    
    # Get the percentage of each dataset that's made of each cluster size
    train_clustersgb['n_proteins'] = train_clustersgb['cluster size (n_members)']*train_clustersgb['n_clusters']    # proteins per cluster * n clusters = # proteins
    train_clustersgb['percent_proteins'] = train_clustersgb['n_proteins']/sum(train_clustersgb['n_proteins'])
    val_clustersgb['n_proteins'] = val_clustersgb['cluster size (n_members)']*val_clustersgb['n_clusters']
    val_clustersgb['percent_proteins'] = val_clustersgb['n_proteins']/sum(val_clustersgb['n_proteins'])
    test_clustersgb['n_proteins'] = test_clustersgb['cluster size (n_members)']*test_clustersgb['n_clusters']
    test_clustersgb['percent_proteins'] = test_clustersgb['n_proteins']/total_test_proteins
    benchmark_clustersgb['n_proteins'] = benchmark_clustersgb['cluster size (n_members)']*benchmark_clustersgb['n_clusters']
    benchmark_clustersgb['percent_proteins'] = benchmark_clustersgb['n_proteins']/total_test_proteins
    
    # Specially mark the benchmark clusters because these can't be reallocated
    if ax is None:
        fig, ax = plt.subplots(figsize=(18, 6))
        
    ax.plot(train_clustersgb['cluster size (n_members)'],train_clustersgb['percent_proteins'],linestyle='None',marker='.',color=colormap['train'],label='train')
    ax.plot(val_clustersgb['cluster size (n_members)'],val_clustersgb['percent_proteins'],linestyle='None',marker='.',color=colormap['val'],label='val')
    ax.plot(test_clustersgb['cluster size (n_members)'],test_clustersgb['percent_proteins'],linestyle='None',marker='.',color=colormap['test'],label='test')
    ax.plot(benchmark_clustersgb['cluster size (n_members)'],benchmark_clustersgb['percent_proteins'],
            marker='o',                
            linestyle='None',          
            markerfacecolor=colormap['test'],      # fill same as test
            markeredgecolor='black',    # outline black
            markeredgewidth=1.5,        
            label='benchmark'
        )
    ax.set_ylabel('Percentage of Proteins in Dataset', fontsize=24)
    ax.set_xlabel('Cluster Size', fontsize=24)
    ax.tick_params(axis='x', labelsize=24)  # Customize x-axis tick label size
    ax.tick_params(axis='y', labelsize=24)  # Customize y-axis tick label size

    ax.legend(fontsize=24,markerscale=4)
    
    # save the figure
    if savepath is not None:
        plt.tight_layout()
        plt.savefig(savepath)
        log_update(f"\tSaved figure to {savepath}") 

def get_avg_embeddings_for_tsne(train_sequences, val_sequences, test_sequences, embedding_path='fuson_db_embeddings/fuson_db_esm2_t33_650M_UR50D_avg_embeddings.pkl'):
    embeddings = {}
    
    try:
        with open(embedding_path, 'rb') as f:
            embeddings = pickle.load(f)
            
        train_embeddings = [v for k, v in embeddings.items() if k in train_sequences]
        val_embeddings = [v for k, v in embeddings.items() if k in val_sequences]
        test_embeddings = [v for k, v in embeddings.items() if k in test_sequences]
        
        return train_embeddings, val_embeddings, test_embeddings
    except:
        print("could not open embeddings")


def visualize_splits_tsne(train_sequences, val_sequences, test_sequences, colormap, esm_type="esm2_t33_650M_UR50D", embedding_path="fuson_db_embeddings/fuson_db_esm2_t33_650M_UR50D_avg_embeddings.pkl", savepath='../data/splits/tsne_plot.png',ax=None):
    """
    Generate a t-SNE plot of embeddings for train, test, and validation.
    """
    log_update('\nMaking t-SNE plot of train, val, and test embeddings')
    # Combine the embeddings into one array
    train_embeddings, val_embeddings, test_embeddings = get_avg_embeddings_for_tsne(train_sequences, val_sequences, test_sequences, embedding_path=embedding_path)
    embeddings = np.concatenate([train_embeddings, val_embeddings, test_embeddings])

    # Labels for the embeddings
    labels = ['train'] * len(train_embeddings) + ['val'] * len(val_embeddings) + ['test'] * len(test_embeddings)

    # Perform t-SNE
    tsne = TSNE(n_components=2, random_state=42)
    tsne_results = tsne.fit_transform(embeddings)

    # Convert t-SNE results into a DataFrame
    tsne_df = pd.DataFrame(data=tsne_results, columns=['TSNE_1', 'TSNE_2'])
    tsne_df['label'] = labels

    # Plotting
    if ax is None:
        fig, ax = plt.subplots(figsize=(10, 8))
    
    # Scatter plot for each set
    for label, color in colormap.items():
        subset = tsne_df[tsne_df['label'] == label].reset_index(drop=True)
        ax.scatter(subset['TSNE_1'], subset['TSNE_2'], c=color, label=label.capitalize(), alpha=0.6)
    
    ax.set_title(f't-SNE of {esm_type} Embeddings')
    ax.set_xlabel('t-SNE Dimension 1')
    ax.set_ylabel('t-SNE Dimension 2')
    ax.legend(fontsize=24, markerscale=2)
    ax.grid(True)
    
    # Save the figure if savepath is provided
    if savepath:
        plt.tight_layout()
        fig.savefig(savepath)

def visualize_splits_shannon_entropy(train_sequences, val_sequences, test_sequences, colormap, savepath='../data/splits/shannon_entropy_plot.png',axes=None):
    """
    Generate Shannon entropy plots for train, validation, and test sets.
    """
    log_update('\nMaking histogram of Shannon Entropy distributions')
    train_entropy = [calculate_shannon_entropy(seq) for seq in train_sequences]
    val_entropy = [calculate_shannon_entropy(seq) for seq in val_sequences]
    test_entropy = [calculate_shannon_entropy(seq) for seq in test_sequences]
    
    if axes is None:
        fig, axes = plt.subplots(1, 3, figsize=(18, 6))
    
    axes[0].hist(train_entropy, bins=20, edgecolor='k', color=colormap['train'])
    axes[0].set_title(f'Train Set (n={len(train_entropy)})', fontsize=24)
    axes[0].set_xlabel('Shannon Entropy', fontsize=24)
    axes[0].set_ylabel('Frequency', fontsize=24)
    axes[0].grid(True)
    axes[0].set_axisbelow(True)
    axes[0].tick_params(axis='x', labelsize=24)  
    axes[0].tick_params(axis='y', labelsize=24)  
    
    axes[1].hist(val_entropy, bins=20, edgecolor='k', color=colormap['val'])
    axes[1].set_title(f'Validation Set (n={len(val_entropy)})', fontsize=24)
    axes[1].set_xlabel('Shannon Entropy', fontsize=24)
    axes[1].grid(True)
    axes[1].set_axisbelow(True)
    axes[1].tick_params(axis='x', labelsize=24)  
    axes[1].tick_params(axis='y', labelsize=24)  
    
    axes[2].hist(test_entropy, bins=20, edgecolor='k', color=colormap['test'])
    axes[2].set_title(f'Test Set (n={len(test_entropy)})', fontsize=24)
    axes[2].set_xlabel('Shannon Entropy', fontsize=24)
    axes[2].grid(True)
    axes[2].set_axisbelow(True)
    axes[2].tick_params(axis='x', labelsize=24)  
    axes[2].tick_params(axis='y', labelsize=24)  
    
    if savepath is not None:
        plt.tight_layout()
        plt.savefig(savepath)

def visualize_splits_aa_composition(train_sequences, val_sequences, test_sequences,colormap, savepath='../data/splits/aa_comp.png',ax=None):
    log_update('\nMaking bar plot of AA composition across each set')
    train_comp = calculate_aa_composition(train_sequences)
    val_comp = calculate_aa_composition(val_sequences)
    test_comp = calculate_aa_composition(test_sequences)

    # Create DataFrame
    comp_df = pd.DataFrame([train_comp, val_comp, test_comp], index=['train', 'val', 'test']).T
    colors = [colormap[col] for col in comp_df.columns]

    # Plotting
    #fig, ax = plt.subplots(figsize=(12, 6))
    if ax is None:
        fig, ax = plt.subplots(figsize=(12, 6))
    else:
        fig = ax.get_figure()
        
    comp_df.plot(kind='bar', color=colors, ax=ax)
    ax.set_title('Amino Acid Composition Across Datasets', fontsize=24)
    ax.set_xlabel('Amino Acid', fontsize=24)
    ax.set_ylabel('Relative Frequency', fontsize=24)
    ax.tick_params(axis='x', labelsize=24)  # Customize x-axis tick label size
    ax.tick_params(axis='y', labelsize=24)  # Customize y-axis tick label size
    ax.legend(fontsize=16, markerscale=2)
    
    if savepath is not None:
        fig.savefig(savepath)

def visualize_splits(train_clusters, val_clusters, test_clusters, benchmark_cluster_reps, train_color='#0072B2',val_color='#009E73',test_color='#E69F00',esm_embeddings_path=None, onehot_embeddings_path=None):
    colormap = {
        'train': train_color,
        'val': val_color,
        'test': test_color
    }
    # Add columns for plotting
    train_clusters['member length'] = train_clusters['member seq'].str.len()
    val_clusters['member length'] = val_clusters['member seq'].str.len()
    test_clusters['member length'] = test_clusters['member seq'].str.len()
    
    # Prepare lengths and seqs for plotting
    train_lengths = train_clusters['member length'].tolist()
    val_lengths = val_clusters['member length'].tolist()
    test_lengths = test_clusters['member length'].tolist()
    train_sequences = train_clusters['member seq'].tolist()
    val_sequences = val_clusters['member seq'].tolist()
    test_sequences = test_clusters['member seq'].tolist()
    
    # Create a combined figure with 3 rows and 3 columns
    fig_combined, axs = plt.subplots(3, 3, figsize=(24, 18))

    # Make the three visualization plots for saving TOGETHER
    visualize_splits_hist(train_lengths,val_lengths,test_lengths,colormap, savepath=None,axes=axs[0])
    visualize_splits_shannon_entropy(train_sequences,val_sequences,test_sequences,colormap,savepath=None,axes=axs[1])
    visualize_splits_scatter(train_clusters, val_clusters, test_clusters, benchmark_cluster_reps, colormap, savepath=None, ax=axs[2, 0])
    visualize_splits_aa_composition(train_sequences,val_sequences,test_sequences, colormap, savepath=None, ax=axs[2, 1])
    if not(esm_embeddings_path is None) and os.path.exists(esm_embeddings_path):
        visualize_splits_tsne(train_sequences, val_sequences, test_sequences, colormap, savepath=None, ax=axs[2, 2])
    else:
    # Leave the last subplot blank
        axs[2, 2].axis('off')

    plt.tight_layout()
    fig_combined.savefig('../data/splits/combined_plot.png')
    
    # Make the three visualization plots for saving separately
    visualize_splits_hist(train_clusters['member length'].tolist(), val_clusters['member length'].tolist(), test_clusters['member length'].tolist(),colormap)
    visualize_splits_scatter(train_clusters, val_clusters, test_clusters, benchmark_cluster_reps, colormap)
    visualize_splits_aa_composition(train_clusters['member seq'].tolist(), val_clusters['member seq'].tolist(), test_clusters['member seq'].tolist(),colormap)
    visualize_splits_shannon_entropy(train_sequences,val_sequences,test_sequences,colormap)
    if not(esm_embeddings_path is None) and os.path.exists(esm_embeddings_path):
        visualize_splits_tsne(train_clusters['member seq'].tolist(), val_clusters['member seq'].tolist(), test_clusters['member seq'].tolist(),colormap)
 
def main():
    set_font()
    train_clusters = pd.read_csv('splits/train_cluster_split.csv')
    val_clusters = pd.read_csv('splits/val_cluster_split.csv')
    test_clusters = pd.read_csv('splits/test_cluster_split.csv')
    
    clusters = pd.concat([train_clusters,val_clusters,test_clusters])
    
    fuson_db = pd.read_csv('fuson_db.csv')
    # Get the sequence IDs of all clustered benchmark sequences. 
    benchmark_seq_ids = fuson_db.loc[fuson_db['benchmark'].notna()]['seq_id']
    # Use benchmark_seq_ids to find which clusters contain benchmark sequences.
    benchmark_cluster_reps = clusters.loc[clusters['member seq_id'].isin(benchmark_seq_ids)]['representative seq_id'].unique().tolist()
    
    visualize_splits(train_clusters, val_clusters, test_clusters, benchmark_cluster_reps,
                         esm_embeddings_path='fuson_db_embeddings/fuson_db_esm2_t33_650M_UR50D_avg_embeddings.pkl', onehot_embeddings_path=None)

if __name__ == "__main__":
    main()