Oncodrive3D 1.0.4__py3-none-any.whl

scripts/main.py

@@ -0,0 +1,650 @@
+#!/usr/bin/env python
+
+"""
+Oncodrive3D is a fast and accurate computational method designed to analyze 
+patterns of somatic mutation across tumors, with the goal of identifying 
+three-dimensional (3D) clusters of missense mutations and detecting genes 
+under positive selection. The method leverages AlphaFold 2-predicted protein 
+structures and Predicted Aligned Error (PAE) to define residue contacts 
+within the protein's 3D space. When available, it also integrates mutational 
+profiles to build an accurate background model of neutral mutagenesis, which 
+is used to score potential clusters and simulate synthetic mutations. 
+By applying a novel rank-based statistical approach, Oncodrive3D scores 
+potential 3D clusters and computes empirical p-values."
+"""
+
+import os
+import click
+import daiquiri
+import numpy as np
+
+from scripts import __logger_name__, __version__
+from scripts.globals import DATE, setup_logging_decorator, startup_message
+
+logger = daiquiri.getLogger(__logger_name__)
+
+
+@click.group(context_settings={'help_option_names': ['-h', '--help']})
+@click.version_option(__version__)
+def oncodrive3D():
+    """
+    Oncodrive3D: software for the identification of 3D-clustering 
+    of missense mutations for cancer driver genes detection.
+    """
+    pass
+
+
+# =============================================================================
+#                               BUILD DATASETS
+# =============================================================================
+
+@oncodrive3D.command(context_settings=dict(help_option_names=['-h', '--help']),
+                     help="Build datasets - Required once after installation.")
+@click.option("-o", "--output_dir", 
+              help="Directory where to save the files", type=str, default='datasets')
+@click.option("-s", "--organism", type=click.Choice(["Homo sapiens", 'human', "Mus musculus", 'mouse']), 
+              help="Organism name", default="Homo sapiens")
+@click.option("-m", "--mane", 
+              help="Use structures predicted from MANE Select transcripts (Homo sapiens only)", is_flag=True)
+@click.option("-M", "--mane_version", default=1.3, 
+              help="Version of the MANE Select release from NCBI")
+@click.option("-d", "--distance_threshold", type=click.INT, default=10,
+              help="Distance threshold (Å) to define contact between amino acids")
+@click.option("-c", "--cores", type=click.IntRange(min=1, max=len(os.sched_getaffinity(0)), clamp=False), default=len(os.sched_getaffinity(0)),
+              help="Number of cores to use in the computation")
+@click.option("--af_version", type=click.IntRange(min=1, max=4, clamp=False), default=4,
+              help="Version of AlphaFold 2 predictions")
+@click.option("-y", "--yes", 
+              help="No interaction", is_flag=True)
+@click.option("-v", "--verbose", 
+              help="Verbose", is_flag=True)
+@setup_logging_decorator
+def build_datasets(output_dir,
+                   organism,
+                   mane,
+                   distance_threshold,
+                   cores, 
+                   af_version,
+                   mane_version,
+                   yes,
+                   verbose):
+    """"Build datasets necessary to run Oncodrive3D."""
+    
+    from scripts.datasets.build_datasets import build
+    
+    startup_message(__version__, "Initializing building datasets..")
+
+    logger.info(f"Current working directory: {os.getcwd()}")
+    logger.info(f"Build folder path: {output_dir}")
+    logger.info(f"Organism: {organism}")
+    logger.info(f"MANE Select: {mane}")
+    logger.info(f"Distance threshold: {distance_threshold}Å")
+    logger.info(f"CPU cores: {cores}")
+    logger.info(f"AlphaFold version: {af_version}")
+    logger.info(f"MANE version: {mane_version}")
+    logger.info(f"Verbose: {verbose}")
+    logger.info(f'Log path: {os.path.join(output_dir, "log")}')
+    logger.info("")
+    
+    build(output_dir,
+          organism,
+          mane,
+          distance_threshold,
+          cores,
+          af_version,
+          mane_version)
+
+
+
+# =============================================================================
+#                                     RUN
+# =============================================================================
+
+@oncodrive3D.command(context_settings=dict(help_option_names=['-h', '--help']),
+                     help="Run 3D-clustering analysis.")
+@click.option("-i", "--input_path", type=click.Path(exists=True), required=True, 
+              help="Path of the MAF file (or direct VEP output) used as input")
+@click.option("-p", "--mut_profile_path", type=click.Path(exists=True), 
+              help="Path of the mutation profile (192 trinucleotide contexts) used as optional input")
+@click.option("-m", "--mutability_config_path", type=click.Path(exists=True), 
+              help="Path of the config file with information on mutability")
+@click.option("-o", "--output_dir", type=str, default='output', 
+              help="Path to output directory")
+@click.option("-d", "--data_dir", type=click.Path(exists=True), default = os.path.join('datasets'), 
+              help="Path to datasets")
+@click.option("-n", "--n_iterations", type=int, default=10000, 
+              help="Number of densities to be simulated")
+@click.option("-a", "--alpha", type=float, default=0.01, 
+              help="Significant threshold for the p-value of res and gene")
+@click.option("-P", "--cmap_prob_thr", type=float, default=0.5,
+              help="Threshold to define AAs contacts based on distance on predicted structure and PAE")
+@click.option("-c", "--cores", type=click.IntRange(min=1, max=len(os.sched_getaffinity(0)), clamp=False), default=len(os.sched_getaffinity(0)),
+              help="Set the number of cores to use in the computation")
+@click.option("-s", "--seed", type=int,
+              help="Set seed to ensure reproducible results")
+@click.option("-v", "--verbose", 
+              help="Verbose", is_flag=True)
+@click.option("-t", "--cancer_type", 
+              help="Cancer type", type=str)
+@click.option("-C", "--cohort", 
+              help="Name of the cohort", type=str)
+@click.option("--no_fragments", is_flag=True, 
+              help="Disable processing of fragmented (AF-F) proteins")
+@click.option("--only_processed", is_flag=True,
+              help="Include only processed genes in the output")
+@click.option("--thr_mapping_issue", type=float, default=0.1,
+              help="Threshold to filter out genes by the ratio of mutations with mapping issue (out of structure, WT AA mismatch, zero prob to mutate). Threshold of 1 disable any WT AA mismatch mutations filtering.")
+@click.option("--o3d_transcripts", is_flag=True,
+              help="Filter mutations by keeping transcripts included in Oncodrive3D built sequence dataframe. Only if input file (--i) is a raw VEP output")
+@click.option("--use_input_symbols", is_flag=True,
+              help="Update HUGO symbols in Oncodrive3D built datasets by using input file entries. Only if input file (--i) is a raw VEP output")
+@click.option("--mane", is_flag=True,
+              help="If multiple structures are associated to the same HUGO symbol in the input file, use the MANE ones.")
+@click.option("--sample_info", is_flag=True,
+              help="Include sample information in position-level result (currently unavailable).")                  # TODO: enable sample info in output
+@setup_logging_decorator
+def run(input_path,
+        mut_profile_path,
+        mutability_config_path,
+        output_dir,
+        data_dir,
+        n_iterations,
+        alpha,
+        cmap_prob_thr,
+        cores,
+        seed,
+        verbose,
+        cancer_type,
+        cohort,
+        no_fragments,
+        only_processed,
+        thr_mapping_issue,
+        o3d_transcripts,
+        use_input_symbols,
+        mane,
+        sample_info):
+    """Run Oncodrive3D."""
+    
+    from scripts.run.clustering import run_clustering
+    
+    # Initialize
+    plddt_path = os.path.join(data_dir, "confidence.tsv")
+    cmap_path = os.path.join(data_dir, "prob_cmaps")
+    seq_df_path = os.path.join(data_dir, "seq_for_mut_prob.tsv")
+    pae_path = os.path.join(data_dir, "pae")
+    cancer_type = cancer_type if cancer_type else np.nan
+    cohort = cohort if cohort else f"cohort_{DATE}"
+    path_prob = mut_profile_path if mut_profile_path else "Not provided, mutabilities will be used" if mutability_config_path else "Not provided, uniform distribution will be used"
+    path_mutability_config = mutability_config_path if mutability_config_path else "Not provided, mutabilities will not be used"
+
+    # Log
+    startup_message(__version__, "Initializing analysis..")
+
+    logger.info(f"Input MAF: {input_path}")
+    logger.info(f"Input mut profile: {path_prob}")
+    logger.info(f"Input mutability config: {path_mutability_config}")
+    logger.info(f"Build directory: {data_dir}")
+    logger.info(f"Output directory: {output_dir}")
+    logger.debug(f"Path to CMAPs: {cmap_path}")
+    logger.debug(f"Path to DNA sequences: {seq_df_path}")
+    logger.debug(f"Path to PAE: {pae_path}")
+    logger.debug(f"Path to pLDDT scores: {plddt_path}")
+    logger.info(f"CPU cores: {cores}")
+    logger.info(f"Iterations: {n_iterations}")
+    logger.info(f"Significant level: {alpha}")
+    logger.info(f"Probability threshold for CMAPs: {cmap_prob_thr}")
+    logger.info(f"Cohort: {cohort}")
+    logger.info(f"Cancer type: {cancer_type}")
+    logger.info(f"Disable fragments: {no_fragments}")
+    logger.info(f"Output only processed genes: {only_processed}")
+    logger.info(f"Ratio threshold mutations with mapping issue: {thr_mapping_issue}")
+    logger.info(f"Seed: {seed}")
+    logger.info(f"Filter input by Oncodrive3D transcripts: {o3d_transcripts}")
+    logger.info(f"Use HUGO symbols of input file: {use_input_symbols}")
+    logger.info(f"Prioritize MANE transcripts when using input HUGO symbols: {mane}")
+    logger.info(f"Include sample informations in output: {sample_info}")
+    logger.info(f"Verbose: {verbose}")
+    logger.info(f'Log path: {os.path.join(output_dir, "log")}')
+    logger.info("")
+
+    run_clustering(input_path,
+                    mut_profile_path,
+                    mutability_config_path,
+                    output_dir,  
+                    cmap_path,
+                    seq_df_path,
+                    plddt_path,
+                    pae_path,                    
+                    n_iterations,
+                    alpha,
+                    cmap_prob_thr,
+                    cores,
+                    seed,
+                    verbose,
+                    cancer_type,
+                    cohort,
+                    no_fragments,
+                    only_processed,
+                    thr_mapping_issue,
+                    o3d_transcripts,
+                    use_input_symbols,
+                    mane,
+                    sample_info)
+
+               
+
+# =============================================================================
+#                              BUILD ANNOTATIONS
+# =============================================================================
+
+@oncodrive3D.command(context_settings=dict(help_option_names=['-h', '--help']),
+               help="Build annotations - Required (once) only to plot annotations.")
+@click.option("-d", "--data_dir", help="Path to datasets", type=str, required=True)
+@click.option("-o", "--output_dir", help="Path to dir where to store annotations", type=str, default="annotations")
+@click.option("-g", "--ddg_dir", help="Path to custom ddG predictions", type=str)
+#@click.option("-S", "--path_pdb_tool_sif", help="Path to the PDB_Tool SIF", type=str, required=True) 
+@click.option("-s", "--organism", type=click.Choice(["Homo sapiens", 'human', "Mus musculus", 'mouse']), help="Organism name", default="Homo sapiens")
+@click.option("-c", "--cores", type=click.IntRange(min=1, max=len(os.sched_getaffinity(0)), clamp=False), default=len(os.sched_getaffinity(0)),
+              help="Number of cores to use in the computation")
+@click.option("-y", "--yes", help="No interaction", is_flag=True)
+@click.option("-v", "--verbose", help="Verbose", is_flag=True)
+@setup_logging_decorator
+def build_annotations(data_dir,
+                      output_dir,
+                      ddg_dir,
+                      #path_pdb_tool_sif,
+                      organism,
+                      cores,
+                      yes,
+                      verbose):
+    """
+    Build datasets to plot protein annotations.
+    """
+
+    startup_message(__version__, "Initializing building annotations..")
+    
+    logger.info(f"Output directory: {output_dir}")
+    logger.info(f"Path to datasets: {data_dir}")
+    logger.info(f"Path to custom ddG predictions: {ddg_dir}")
+    #logger.info(f"Path to PDB_Tool SIF: {path_pdb_tool_sif}")
+    logger.info(f"Organism: {organism}")
+    logger.info(f"Cores: {cores}")
+    logger.info(f"Verbose: {bool(verbose)}")
+    logger.info(f'Log path: {os.path.join(output_dir, "log")}')
+    logger.info("")
+    
+    from scripts.plotting.build_annotations import get_annotations
+
+    get_annotations(data_dir, 
+                    output_dir, 
+                    ddg_dir,
+                    #path_pdb_tool_sif,
+                    organism,
+                    cores)
+
+
+
+# =============================================================================
+#                                    PLOT
+# =============================================================================
+
+@oncodrive3D.command(context_settings=dict(help_option_names=['-h', '--help']),
+               help="Generate plots for a quick interpretation of the 3D-clustering analysis.")
+@click.option("-g", "--gene_result_path", type=click.Path(exists=True), required=True,
+              help="Path to genes-level O3D result")
+@click.option("-p", "--pos_result_path", type=click.Path(exists=True), required=True,
+              help="Path to positions-level O3D result")
+@click.option("-i", "--maf_path", type=click.Path(exists=True), required=True,
+              help="Path to input mutations file")
+@click.option("-m", "--miss_prob_path", type=click.Path(exists=True), required=True,
+              help="Path to missense mutations probability dictionary")
+@click.option("-s", "--seq_df_path", type=click.Path(exists=True), required=True,
+              help="Path to dataframe of sequences")
+@click.option("-d", "--datasets_dir", type=click.Path(exists=True), required=True,
+              help="Path to datasets directory")
+@click.option("-a", "--annotations_dir", type=click.Path(exists=True), required=True, 
+              help="Path to annotations directory")
+@click.option("-o", "--output_dir", default="./",
+              help="Path to output directory where to save plots")
+@click.option("-c", "--cohort", 
+              help="Cohort name", type=str, required=True)
+@click.option("--title",                                                                              ## Might be redundant
+              help="Plot title", type=str)
+@click.option("--maf_for_nonmiss_path", type=click.Path(exists=True), 
+              help="Path to input mutations file including non-missense mutations")
+@click.option("--lst_summary_tracks", type=str,
+              help="List of tracks to be included in the summary plot (e.g., score,miss_count,clusters)", 
+              default="score,miss_count,res_count,res_clust_mut,clusters")
+@click.option("--lst_summary_hratios", type=str,
+              help="List of float to define horizontal ratio of each track of the summary plot") 
+@click.option("--lst_gene_tracks", type=str,
+              help="List of tracks to be included in the gene plots (e.g., miss_count,miss_prob,score)",
+              default="miss_count,miss_prob,score,clusters,ddg,disorder,pacc,ptm,site,sse,pfam,prosite,membrane,motif")
+@click.option("--lst_gene_hratios", type=str,
+              help="List of floats to define horizontal ratio of each track of the gene plot") 
+@click.option("--summary_fsize_x", help="Figure size x-axis for summary plots (dynamically adjusted)", type=float, default=0.5)
+@click.option("--summary_fsize_y", help="Figure size y-axis for summary plots", type=int, default=8)
+@click.option("--gene_fsize_x", help="Figure size x-axis for gene plots", type=int, default=24)
+@click.option("--gene_fsize_y", help="Figure size y-axis for gene plots", type=int, default=12)
+@click.option("--summary_alpha", help="Alpha value for score track in summary plot", type=float, default=0.7)
+@click.option("--dist_thr", help="Threshold of ratios to avoid clashing feature names (e.g., domains and motifs)", type=float, default=0.1)
+@click.option("--genes", help="List of genes to be analysed in the report (e.g., --genes TP53,KRAS,PIK3CA)", type=str)
+@click.option("--c_genes_only", help="Generate gene plots only for significant genes (use --no-c_genes_only to disable)", is_flag=True, default=True)
+@click.option("--max_n_genes", help="Max number of genes to plot", type=int, default=30)
+@click.option("--volcano_top_n", help="Top associations to annotate in volcano plot", type=int, default=15)
+@click.option("--volcano_fsize_x", help="Figure size x-axis for volcano plot", type=float, default=10)
+@click.option("--volcano_fsize_y", help="Figure size y-axis for volcano plot", type=float, default=6)
+@click.option("--volcano_subplots_fsize_x", help="Figure size x-axis for volcano subplots (dynamically adjusted)", type=float, default=3.2)
+@click.option("--volcano_subplots_fsize_y", help="Figure size y-axis for volcano subplots (dynamically adjusted)", type=float, default=3)
+@click.option("--log_odds_fsize_x", help="Figure size x-axis for log odds plot (dynamically adjusted)", type=float, default=1.7)
+@click.option("--log_odds_fsize_y", help="Figure size y-axis for log odds plot (dynamically adjusted)", type=float, default=3.6)
+@click.option("--output_csv", help="Output csv file including annotated Oncodrive3D result", is_flag=True)
+@click.option("--output_all_pos", help="Include all position (including non-mutated ones) in the Oncodrive3D enriched result", is_flag=True)
+@click.option("-v", "--verbose", help="Verbose", is_flag=True)
+@setup_logging_decorator
+def plot(gene_result_path,
+         pos_result_path,
+         maf_path,
+         miss_prob_path,
+         seq_df_path,
+         datasets_dir,
+         annotations_dir,
+         output_dir,
+         cohort,
+         title,
+         maf_for_nonmiss_path,
+         lst_summary_tracks,
+         lst_summary_hratios,
+         lst_gene_tracks,
+         lst_gene_hratios,
+         summary_fsize_x,
+         summary_fsize_y,
+         gene_fsize_x,
+         gene_fsize_y,
+         summary_alpha,
+         dist_thr, 
+         genes,
+         c_genes_only,
+         max_n_genes,
+         volcano_top_n,
+         volcano_fsize_x,
+         volcano_fsize_y,
+         volcano_subplots_fsize_x,
+         volcano_subplots_fsize_y,
+         log_odds_fsize_x,
+         log_odds_fsize_y,
+         output_csv,
+         output_all_pos,
+         verbose):
+    """"Generate summary and individual gene plots for a quick interpretation of the 3D-clustering analysis."""
+
+    from scripts.plotting.plot import generate_plots
+    from scripts.plotting.utils import init_plot_pars, parse_lst_tracks
+
+    startup_message(__version__, "Starting plot generation..")
+    logger.info(f"O3D genes-result: {gene_result_path}")
+    logger.info(f"O3D positions-result: {pos_result_path}")
+    logger.info(f"O3D input mutations: {maf_path}")
+    logger.info(f"O3D missense mut prob: {miss_prob_path}")
+    logger.info(f"O3D sequences df: {seq_df_path}")
+    logger.info(f"O3D datasets: {datasets_dir}")
+    logger.info(f"O3D annotations: {annotations_dir}")
+    logger.info(f"Output: {output_dir}")
+    logger.info(f"Cohort: {cohort}")
+    logger.info(f"Title: {title}")
+    logger.info(f"Input mutations including non-missense: {maf_for_nonmiss_path}")
+    logger.info(f"Custom summary plot tracks: {lst_summary_tracks}")
+    logger.info(f"Custom summary plot h-ratios: {lst_summary_hratios}")
+    logger.info(f"Custom gene plots tracks: {lst_gene_tracks}")
+    logger.info(f"Custom gene plots h-ratios: {lst_gene_hratios}")
+    logger.info(f"Summary plot fsize_x (dynamically adjusted): {summary_fsize_x}")
+    logger.info(f"Summary plot fsize_y: {summary_fsize_y}")
+    logger.info(f"Gene plots fsize_x: {gene_fsize_x}")
+    logger.info(f"Gene plots fsize_y: {gene_fsize_y}")
+    logger.info(f"Volcano plot fsize_x: {volcano_fsize_x}")
+    logger.info(f"Volcano plot fsize_y: {volcano_fsize_y}")
+    logger.info(f"Volcano subplot fsize_x (dynamically adjusted): {volcano_subplots_fsize_x}")
+    logger.info(f"Volcano subplot fsize_y (dynamically adjusted): {volcano_subplots_fsize_y}")
+    logger.info(f"Log odds plot fsize_x (dynamically adjusted): {log_odds_fsize_x}")
+    logger.info(f"Log odds plot fsize_y (dynamically adjusted): {log_odds_fsize_y}")
+    logger.info(f"Summary plot score alpha: {summary_alpha}")
+    logger.info(f"Threshold for clashing feat: {dist_thr}")
+    logger.info(f"Subset of genes: {genes}")
+    logger.info(f"Gene plots for significant genes only: {bool(c_genes_only)}")
+    logger.info(f"Max number of genes to plot: {max_n_genes}")
+    logger.info(f"Volcano plot top associations to annotate: {volcano_top_n}")
+    logger.info(f"Output csv file: {bool(output_csv)}")
+    logger.info(f"Include non-mutated positions in csv file: {bool(output_all_pos)}")
+    logger.info(f"Verbose: {bool(verbose)}")
+    logger.info(f'Log path: {os.path.join(output_dir, "log")}')
+    logger.info("")
+
+    lst_summary_tracks = parse_lst_tracks(lst_summary_tracks, plot_type="summary")
+    lst_gene_tracks = parse_lst_tracks(lst_gene_tracks, plot_type="gene")
+    plot_pars = init_plot_pars(summary_fsize_x=summary_fsize_x,
+                               summary_fsize_y=summary_fsize_y,
+                               gene_fsize_x=gene_fsize_x, 
+                               gene_fsize_y=gene_fsize_y, 
+                               volcano_fsize_x=volcano_fsize_x,
+                               volcano_fsize_y=volcano_fsize_y,
+                               volcano_subplots_fsize_x=volcano_subplots_fsize_x,
+                               volcano_subplots_fsize_y=volcano_subplots_fsize_y,
+                               log_odds_fsize_x=log_odds_fsize_x,
+                               log_odds_fsize_y=log_odds_fsize_y,
+                               dist_thr=dist_thr,
+                               summary_alpha=summary_alpha,
+                               lst_summary_tracks=lst_summary_tracks,
+                               lst_summary_hratios=lst_summary_hratios,
+                               lst_gene_annot=lst_gene_tracks, 
+                               lst_gene_hratios=lst_gene_hratios,
+                               volcano_top_n=volcano_top_n)
+
+    generate_plots(gene_result_path=gene_result_path,
+                  pos_result_path=pos_result_path,
+                  maf_path=maf_path,
+                  miss_prob_path=miss_prob_path,
+                  seq_df_path=seq_df_path,
+                  cohort=cohort,
+                  datasets_dir=datasets_dir,
+                  annotations_dir=annotations_dir,
+                  output_dir=output_dir,
+                  plot_pars=plot_pars,
+                  maf_path_for_nonmiss=maf_for_nonmiss_path,
+                  c_genes_only=c_genes_only,
+                  n_genes=max_n_genes,
+                  lst_genes=genes,
+                  save_plot=True,
+                  show_plot=False,
+                  save_csv=output_csv,
+                  include_all_pos=output_all_pos,
+                  title=title)
+
+
+
+# =============================================================================
+#                              COMPARATIVE PLOTS
+# =============================================================================
+
+@oncodrive3D.command(context_settings=dict(help_option_names=['-h', '--help']),
+               help="Generate plots to compare two runs of 3D-clustering analysis.")
+@click.option("-i", "--o3d_result_dir_1", type=click.Path(exists=True), required=True,
+              help="Path to result A directory (including gene- and pos-level result for run A)")
+@click.option("-I", "--o3d_result_dir_2", type=click.Path(exists=True), required=True,
+              help="Path to result B directory (including gene- and pos-level result for run B)")
+@click.option("-c", "--cohort_1", 
+              help="Cohort A name (it should match the basename of the files in o3d_result_dir)", type=str, required=True)
+@click.option("-C", "--cohort_2", 
+              help="Cohort B name (it should match the basename of the files in o3d_result_dir)", type=str, required=True)
+@click.option("-d", "--datasets_dir", type=click.Path(exists=True), required=True,
+              help="Path to datasets directory")
+@click.option("-a", "--annotations_dir", type=click.Path(exists=True), required=True, 
+              help="Path to annotations directory")
+@click.option("-o", "--output_dir", required=True,
+              help="Path to output directory where to save plots")
+@click.option("--maf_path_nonmiss_1", type=click.Path(exists=True), 
+              help="Path to input mutations file A including non-missense mutations")
+@click.option("--maf_path_nonmiss_2", type=click.Path(exists=True), 
+              help="Path to input mutations file B including non-missense mutations (e.g., miss_count,miss_prob,score)")
+@click.option("--lst_tracks", type=str,
+              help="List of tracks to plot", 
+              default="miss_count,miss_prob,score,clusters,ddg,disorder,pacc,ptm,site,sse,pfam,prosite,membrane,motif")
+@click.option("--lst_hratios", type=str,
+              help="List of float to define horizontal ratio of each track of the plot") 
+@click.option("--fsize_x", help="Figure size x-axis", type=float, default=24)
+@click.option("--fsize_y", help="Figure size y-axis", type=float, default=12)
+@click.option("--dist_thr", help="Threshold of ratios to avoid clashing feature names (e.g., domains and motifs)", type=float, default=0.1)
+@click.option("--genes", help="List of genes to be analysed in the report (e.g., --genes TP53,KRAS,PIK3CA)", type=str)
+@click.option("--max_n_genes", help="Max number of genes to plot", type=int, default=30)
+@click.option("--count_mirror", help="Missense mutation count track as mirror image", is_flag=True)
+@click.option("--prob_mirror", help="Missense mutation prob track as mirror image", is_flag=True)
+@click.option("--score_mirror", help="Clustering score track as mirror image", is_flag=True)
+@click.option("-v", "--verbose", help="Verbose", is_flag=True)
+@setup_logging_decorator
+def comparative_plot(o3d_result_dir_1,
+                     cohort_1,
+                     o3d_result_dir_2,
+                     cohort_2,
+                     datasets_dir, 
+                     annotations_dir,
+                     output_dir,
+                     maf_path_nonmiss_1,
+                     maf_path_nonmiss_2,
+                     lst_tracks,
+                     lst_hratios,
+                     fsize_x,
+                     fsize_y,
+                     dist_thr,
+                     count_mirror,
+                     prob_mirror,
+                     score_mirror,
+                     genes,
+                     max_n_genes,
+                     verbose):
+    """"Generate genes comparative plots to comprare two runs of 3D-clustering analysis."""
+
+    from scripts.plotting.plot import generate_comparative_plots
+    from scripts.plotting.utils import init_comp_plot_pars, parse_lst_tracks
+
+    startup_message(__version__, "Starting plot generation..")
+    logger.info(f"Oncodrive3D result A: {o3d_result_dir_1}")
+    logger.info(f"Cohort B: {cohort_1}")
+    logger.info(f"Oncodrive3D result B: {o3d_result_dir_2}")
+    logger.info(f"Cohort B: {cohort_2}")
+    logger.info(f"Oncodrive3D datasets: {datasets_dir}")
+    logger.info(f"Oncodrive3D annotations: {annotations_dir}")
+    logger.info(f"Output: {output_dir}")
+    logger.info(f"Input mutations including non-missense A: {maf_path_nonmiss_1}")
+    logger.info(f"Input mutations including non-missense B: {maf_path_nonmiss_2}")
+    logger.info(f"Custom gene plots tracks: {lst_tracks}")
+    logger.info(f"Custom gene plots h-ratios: {lst_hratios}")
+    logger.info(f"Summary plot fsize_x: {fsize_x}")
+    logger.info(f"Summary plot fsize_y: {fsize_y}")
+    logger.info(f"Threshold for clashing feat: {dist_thr}")
+    logger.info(f"Missense mut as mirror image: {bool(count_mirror)}")
+    logger.info(f"Missense mut prob as mirror image: {bool(prob_mirror)}")
+    logger.info(f"Score as mirror image: {bool(score_mirror)}")
+    logger.info(f"Verbose: {bool(verbose)}")
+    logger.info(f"Subset of genes: {genes}")
+    logger.info(f"Max number of genes to plot: {max_n_genes}")
+    logger.info(f"Verbose: {bool(verbose)}")
+    logger.info(f'Log path: {os.path.join(output_dir, "log")}')
+    logger.info("")
+    
+    lst_tracks = parse_lst_tracks(lst_tracks, plot_type="gene")
+    plot_pars = init_comp_plot_pars(fsize_x=fsize_x,
+                                    fsize_y=fsize_y,
+                                    dist_thr=dist_thr,
+                                    lst_tracks=lst_tracks,
+                                    lst_hratios=lst_hratios,
+                                    count_mirror=count_mirror, 
+                                    score_mirror=score_mirror,
+                                    prob_mirror=prob_mirror)
+
+    generate_comparative_plots(o3d_result_dir_1=o3d_result_dir_1,
+                               cohort_1=cohort_1,
+                               o3d_result_dir_2=o3d_result_dir_2,
+                               cohort_2=cohort_2,
+                               datasets_dir=datasets_dir, 
+                               annotations_dir=annotations_dir,
+                               output_dir=output_dir,
+                               plot_pars=plot_pars,
+                               maf_path_nonmiss_1=maf_path_nonmiss_1,
+                               maf_path_nonmiss_2=maf_path_nonmiss_2,
+                               n_genes=max_n_genes, 
+                               lst_genes=genes)
+
+
+# =============================================================================
+#                              CHIMERAX PLOTS
+# =============================================================================
+
+@oncodrive3D.command(context_settings=dict(help_option_names=['-h', '--help']),
+               help="Generate 3D plots using CHimeraX.")
+@click.option("-o", "--output_dir", 
+              help="Directory where to save the plots", type=str, required=True)
+@click.option("-g", "--gene_result_path", 
+              help="Path to genes-level O3D result", type=click.Path(exists=True), required=True)
+@click.option("-p", "--pos_result_path", 
+              help="Path to positions-level O3D result", type=click.Path(exists=True), required=True)
+@click.option("-d", "--datasets_dir", 
+              help="Path to datasets", type=click.Path(exists=True), required=True)
+@click.option("-s", "--seq_df_path", 
+              help="Path to sequences dataframe", type=click.Path(exists=True), required=True)
+@click.option("-c", "--cohort", 
+              help="Cohort name", default="")
+@click.option("--max_n_genes", help="Maximum number of genes to plot", type=int, default=30)
+@click.option("--pixel_size", help="Pixel size (smaller value is larger number of pixels)", type=float, default=0.08)
+@click.option("--cluster_ext", help="Include extended clusters", is_flag=True)
+@click.option("--fragmented_proteins", help="Include fragmented proteins", is_flag=True)
+@click.option("--transparent_bg", help="Set background as transparent", type=str, is_flag=True)
+@click.option("--chimerax_bin", help="Path to chimerax installation", type=str, default="/usr/bin/chimerax")
+@click.option("-v", "--verbose", help="Verbose", is_flag=True)
+@setup_logging_decorator
+def chimerax_plot(output_dir,
+                  gene_result_path,
+                  pos_result_path,
+                  datasets_dir,
+                  seq_df_path,
+                  cohort,
+                  max_n_genes,
+                  pixel_size,
+                  cluster_ext,
+                  fragmented_proteins,
+                  transparent_bg,
+                  chimerax_bin,
+                  verbose):
+    """"Generate images of structures annotated with clustering metrics."""
+
+    from scripts.plotting.chimerax_plot import generate_chimerax_plot
+
+    startup_message(__version__, "Starting plot generation..")
+    logger.info(f"Output dir: {output_dir}")
+    logger.info(f"Gene result path: {gene_result_path}")
+    logger.info(f"Position result path: {pos_result_path}")
+    logger.info(f"Datasets dir: {datasets_dir}")
+    logger.info(f"Sequence dataframe path: {seq_df_path}")
+    logger.info(f"Cohort: {cohort}")
+    logger.info(f"Max number of genes to plot: {max_n_genes}")
+    logger.info(f"Pixel size: {pixel_size}")
+    logger.info(f"Cluster extended: {cluster_ext}")
+    logger.info(f"Fragmented proteins: {fragmented_proteins}")
+    logger.info(f"Transparent background: {transparent_bg}")
+    logger.info(f"Verbose: {bool(verbose)}")
+    logger.info(f'Log path: {os.path.join(output_dir, "log")}')
+    logger.info("")
+
+    generate_chimerax_plot(output_dir,
+                        gene_result_path,
+                        pos_result_path,
+                        datasets_dir,
+                        seq_df_path,
+                        cohort,
+                        max_n_genes,
+                        pixel_size,
+                        cluster_ext,
+                        fragmented_proteins,
+                        transparent_bg,
+                        chimerax_bin)
+
+if __name__ == "__main__":
+    oncodrive3D()