masster 0.4.22__py3-none-any.whl → 0.5.1__py3-none-any.whl

masster/study/study.py

@@ -52,36 +52,26 @@ import sys
 import polars as pl
 
 # Study-specific imports
-from masster.study.h5 import _load_study5
-from masster.study.h5 import _save_study5
-from masster.study.h5 import _save_study5_compressed
-from masster.study.h5 import _load_ms1
+from masster.study.analysis import analyze_umap
 from masster.study.helpers import _get_consensus_uids
-from masster.study.helpers import _get_feature_uids
-from masster.study.helpers import _get_sample_uids
-from masster.study.helpers import _ensure_features_df_schema_order
+from masster.study.helpers import _get_features_uids
+from masster.study.helpers import _get_samples_uids
 from masster.study.helpers import compress
-from masster.study.helpers import compress_features
-from masster.study.helpers import compress_ms2
-from masster.study.helpers import compress_chrom
-from masster.study.helpers import restore_features
-from masster.study.helpers import restore_chrom
-from masster.study.helpers import restore_ms2
 from masster.study.helpers import decompress
 from masster.study.helpers import fill_reset
 from masster.study.helpers import get_chrom
-from masster.study.helpers import get_sample
+from masster.study.helpers import get_samples
 from masster.study.helpers import get_consensus
 from masster.study.helpers import get_consensus_matches
 from masster.study.helpers import get_consensus_matrix
 from masster.study.helpers import get_orphans
+from masster.study.helpers import get_sample_stats
 from masster.study.helpers import get_gaps_matrix
 from masster.study.helpers import get_gaps_stats
 from masster.study.helpers import align_reset
-from masster.study.helpers import set_folder
-from masster.study.helpers import set_source
-from masster.study.helpers import sample_color
-from masster.study.helpers import sample_color_reset
+from masster.study.helpers import set_study_folder
+from masster.study.helpers import set_samples_source
+from masster.study.helpers import set_samples_color
 from masster.study.helpers import sample_name_replace
 from masster.study.helpers import sample_name_reset
 from masster.study.helpers import samples_select
@@ -94,61 +84,34 @@ from masster.study.helpers import consensus_filter
 from masster.study.helpers import consensus_delete
 from masster.study.load import add
 from masster.study.load import add_sample
-from masster.study.load import _add_samples_batch
-from masster.study.load import _add_sample_optimized
-from masster.study.load import _add_sample_standard
-from masster.study.load import _sample_color_reset_optimized
-from masster.study.load import fill_single
 from masster.study.load import fill
-from masster.study.load import _process_sample_for_parallel_fill
-from masster.study.load import _get_missing_consensus_sample_combinations
 from masster.study.load import load
-from masster.study.load import _load_consensusXML
-from masster.study.load import load_features
-from masster.study.load import sanitize
+from masster.study.load import _load_features
 from masster.study.plot import plot_alignment
 from masster.study.plot import plot_consensus_2d
 from masster.study.plot import plot_samples_2d
 from masster.study.plot import plot_consensus_stats
 from masster.study.plot import plot_chrom
-from masster.study.plot import plot_pca
+from masster.study.plot import plot_samples_pca
+from masster.study.plot import plot_samples_umap
 from masster.study.plot import plot_bpc
 from masster.study.plot import plot_tic
 from masster.study.plot import plot_eic
 from masster.study.plot import plot_rt_correction
 from masster.study.processing import align
 from masster.study.merge import merge
-from masster.study.merge import _reset_consensus_data
-from masster.study.merge import _extract_consensus_features
-from masster.study.merge import _perform_adduct_grouping
-from masster.study.merge import _consensus_cleanup
-from masster.study.merge import _identify_adduct_by_mass_shift
-from masster.study.merge import _finalize_merge
-from masster.study.merge import _count_tight_clusters
 from masster.study.processing import integrate
 from masster.study.processing import find_ms2
 from masster.study.processing import find_iso
 from masster.study.processing import reset_iso
-from masster.study.parameters import store_history
+from masster.study.parameters import update_history
 from masster.study.parameters import get_parameters
 from masster.study.parameters import update_parameters
 from masster.study.parameters import get_parameters_property
 from masster.study.parameters import set_parameters_property
-from masster.study.save import save, save_consensus, _save_consensusXML, save_samples
-from masster.study.export import (
-    export_mgf,
-    export_mztab,
-    export_xlsx,
-    export_parquet,
-    _get_mgf_df,
-)
+from masster.study.save import save, save_consensus, save_samples
+from masster.study.export import export_mgf, export_mztab, export_xlsx, export_parquet
 from masster.study.id import lib_load, identify, get_id, id_reset, lib_reset
-from masster.study.id import (
-    _get_adducts,
-    _calculate_formula_mass_shift,
-    _format_adduct_name,
-    _parse_element_counts,
-)
 
 from masster.logger import MassterLogger
 from masster.study.defaults.study_def import study_defaults
@@ -253,8 +216,24 @@ class Study:
                      For backward compatibility, original signature is supported:
                      Study(folder=..., label=..., log_level=..., log_label=..., log_sink=...)
         """
-        # Initialize default parameters
+        # ===== PARAMETER INITIALIZATION =====
+        auto_load_filename = self._init_parameters(filename, kwargs)
+        
+        # ===== DATA STRUCTURES INITIALIZATION =====
+        self._init_data_structures()
+        
+        # ===== LOGGER INITIALIZATION =====
+        self._init_logger()
+        
+        # ===== AUTO-LOAD FILE IF PROVIDED =====
+        if auto_load_filename is not None:
+            self.load(filename=auto_load_filename)
 
+        # ===== SAMPLE CACHE =====
+        self._samples_cache = {}
+
+    def _init_parameters(self, filename, kwargs):
+        """Initialize parameters and handle filename for auto-loading."""
         # Handle filename parameter for automatic loading
         auto_load_filename = None
         if filename is not None:
@@ -281,13 +260,11 @@ class Study:
                 if hasattr(params, key):
                     params.set(key, value, validate=True)
 
-        # Keeps a pointer to study5 whenever it's saved or loaded
-        self.filename = None
-
-        # Store parameter instance for method access
+        # Store parameter instance and initialize history
+        self.filename = None  # Keeps a pointer to study5 whenever it's saved or loaded
         self.parameters = params
         self.history = {}
-        self.store_history(["study"], params.to_dict())
+        self.update_history(["study"], params.to_dict())
 
         # Set instance attributes (ensure proper string values for logger)
         self.folder = params.folder
@@ -301,10 +278,15 @@ class Study:
         self.log_label = params.log_label + " | " if params.log_label else ""
         self.log_sink = params.log_sink
 
+        # Create folder if it doesn't exist
         if self.folder is not None and not os.path.exists(self.folder):
-            # create the folder if it does not exist
             os.makedirs(self.folder)
+            
+        return auto_load_filename
 
+    def _init_data_structures(self):
+        """Initialize all data structures used by the Study."""
+        # Sample information DataFrame
         self.samples_df = pl.DataFrame(
             {
                 "sample_uid": [],
@@ -337,21 +319,24 @@ class Study:
                 "num_ms2": pl.Int64,
             },
         )
+        
+        # Feature-related data structures
         self.features_maps = []
         self.features_df = pl.DataFrame()
+        
+        # Consensus-related data structures
         self.consensus_ms2 = pl.DataFrame()
         self.consensus_df = pl.DataFrame()
         self.consensus_map = None
         self.consensus_mapping_df = pl.DataFrame()
         self.alignment_ref_index = None
 
-        # Library DataFrame (populated by lib_load)
-        self.lib_df = pl.DataFrame()
+        # Library and identification data structures
+        self.lib_df = pl.DataFrame()  # populated by lib_load
+        self.id_df = pl.DataFrame()   # populated by identify
 
-        # Identification results DataFrame (populated by identify)
-        self.id_df = pl.DataFrame()
-
-        # Initialize independent logger
+    def _init_logger(self):
+        """Initialize the logger for this Study instance."""
         self.logger = MassterLogger(
             instance_type="study",
             level=self.log_level.upper(),
@@ -361,85 +346,68 @@ class Study:
         self.logger.debug(f"Study folder: {self.folder}")
         self.logger.debug(f"Polarity: {self.polarity}")
 
-        # Auto-load study file if filename was provided
-        if auto_load_filename is not None:
-            self.load(filename=auto_load_filename)
-
-        # cache for Sample instances created/loaded by this Study
-        self._samples_cache = {}
-
-    # ===== ATTACH MODULE FUNCTIONS AS CLASS METHODS =====
-    
     # === File I/O Operations ===
     load = load
     save = save
     save_consensus = save_consensus
     save_samples = save_samples
-    sanitize = sanitize
-    set_folder = set_folder
+    set_study_folder = set_study_folder
     
     # === Sample Management ===
     add = add
-    add_folder = add  # backward compatibility alias
     add_sample = add_sample
     
     # === Core Processing Operations ===
     align = align
-    merge = merge
-    find_consensus = merge  # Backward compatibility alias
+    merge = merge   
+    
     find_ms2 = find_ms2
     find_iso = find_iso
     reset_iso = reset_iso
     iso_reset = reset_iso
     integrate = integrate
-    integrate_chrom = integrate  # Backward compatibility alias
+    
     fill = fill
-    fill_chrom = fill  # Backward compatibility alias
-    fill_single = fill_single
-    fill_chrom_single = fill_single  # Backward compatibility alias
+    
     # === Data Retrieval and Access ===
     get_consensus = get_consensus
     get_chrom = get_chrom
-    get_sample = get_sample
+    get_samples = get_samples
     get_consensus_matches = get_consensus_matches
     get_consensus_matrix = get_consensus_matrix
     get_gaps_matrix = get_gaps_matrix
     get_gaps_stats = get_gaps_stats
     get_orphans = get_orphans
+    get_sample_stats = get_sample_stats
     
     # === Data Selection and Filtering ===
     samples_select = samples_select
     samples_delete = samples_delete
+    
     features_select = features_select
     features_filter = features_filter
     features_delete = features_delete
     consensus_select = consensus_select
     consensus_filter = consensus_filter
     consensus_delete = consensus_delete
-    # Backward compatibility aliases
-    filter_consensus = consensus_filter
-    select_consensus = consensus_select
-    filter_features = features_filter
-    select_features = features_select
-    consensus_find = merge
-    
-    # === Sample Metadata and Styling ===
-    set_source = set_source
-    sample_color = sample_color
-    sample_color_reset = sample_color_reset
-    reset_sample_color = sample_color_reset
-    name_replace = sample_name_replace
-    name_reset = sample_name_reset
-    reset_name = sample_name_reset
 
+    # === Sample Metadata and Styling ===
+    set_samples_source = set_samples_source
+    set_samples_color = set_samples_color
+       
+    samples_name_replace = sample_name_replace
+    samples_name_reset = sample_name_reset
+    
+    # Backward compatibility aliases for renamed methods
+    set_folder = set_study_folder
+    set_source = set_samples_source  
+    #sample_color = set_samples_color
+    #get_sample = get_samples
+    #load_features = _load_features
+    store_history = update_history
+    
     # === Data Compression and Storage ===
     compress = compress
-    compress_features = compress_features
-    compress_ms2 = compress_ms2
-    compress_chrom = compress_chrom
-    restore_features = restore_features
-    restore_chrom = restore_chrom
-    restore_ms2 = restore_ms2
     decompress = decompress
     
     # === Reset Operations ===
@@ -453,12 +421,16 @@ class Study:
     plot_chrom = plot_chrom
     plot_consensus_2d = plot_consensus_2d
     plot_consensus_stats = plot_consensus_stats
-    plot_pca = plot_pca
+    plot_samples_pca = plot_samples_pca
+    plot_samples_umap = plot_samples_umap
     plot_samples_2d = plot_samples_2d
     plot_bpc = plot_bpc
     plot_rt_correction = plot_rt_correction
     plot_tic = plot_tic
     plot_eic = plot_eic
+
+    # === Analysis Operations ===
+    analyze_umap = analyze_umap
     
     # === Export Operations ===
     export_mgf = export_mgf
@@ -468,6 +440,11 @@ class Study:
     
     # === Identification and Library Matching ===
     lib_load = lib_load
+    
+    def lib_to_consensus(self, **kwargs):
+        """Create consensus features from library entries."""
+        from masster.study.id import lib_to_consensus as _lib_to_consensus
+        return _lib_to_consensus(self, **kwargs)
     identify = identify
     get_id = get_id
     id_reset = id_reset
@@ -476,45 +453,23 @@ class Study:
     reset_lib = lib_reset
 
     # === Parameter Management ===
-    store_history = store_history
+    update_history = update_history
     get_parameters = get_parameters
     update_parameters = update_parameters
     get_parameters_property = get_parameters_property
     set_parameters_property = set_parameters_property
     
     # === Private/Internal Methods ===
-    _add_samples_batch = _add_samples_batch
-    _add_sample_optimized = _add_sample_optimized
-    _add_sample_standard = _add_sample_standard
-    _sample_color_reset_optimized = _sample_color_reset_optimized
-    _load_study5 = _load_study5
-    _save_study5 = _save_study5
-    _save_study5_compressed = _save_study5_compressed
-    _load_ms1 = _load_ms1
     _get_consensus_uids = _get_consensus_uids
-    _get_feature_uids = _get_feature_uids
-    _get_sample_uids = _get_sample_uids
-    _ensure_features_df_schema_order = _ensure_features_df_schema_order
-    _process_sample_for_parallel_fill = _process_sample_for_parallel_fill
-    _get_missing_consensus_sample_combinations = (
-        _get_missing_consensus_sample_combinations
-    )
-    _load_consensusXML = _load_consensusXML
-    load_features = load_features
-    _save_consensusXML = _save_consensusXML
-    _get_mgf_df = _get_mgf_df
-    _get_adducts = _get_adducts
-    _calculate_formula_mass_shift = _calculate_formula_mass_shift
-    _format_adduct_name = _format_adduct_name
-    _parse_element_counts = _parse_element_counts
+    _get_features_uids = _get_features_uids
+    _get_samples_uids = _get_samples_uids
+    _load_features = _load_features
+    
+    # Note: _load_study5 and _save_study5 are not exposed as class methods
+    # They are used internally by load() and save() methods only
     
     # === Merge Helper Methods ===
-    _reset_consensus_data = _reset_consensus_data
-    _extract_consensus_features = _extract_consensus_features
-    _perform_adduct_grouping = _perform_adduct_grouping
-    _consensus_cleanup = _consensus_cleanup
-    _identify_adduct_by_mass_shift = _identify_adduct_by_mass_shift
-    _finalize_merge = _finalize_merge
+    # (All merge helper methods are now internal to the merge module)
     
     # === Default Parameters ===
     study_defaults = study_defaults
@@ -612,6 +567,83 @@ class Study:
         except Exception as e:
             self.logger.error(f"Failed to reload current module {current_module}: {e}")
 
+    def _sanitize_null_ids(self):
+        """
+        Sanitize null feature_id and consensus_id values by replacing them with new integer IDs.
+        For feature_id: generates large sequential integers that can be converted by merge/align functions.
+        For consensus_id: uses 16-character UUID strings (as expected by merge function).
+        """
+        import uuid
+        import polars as pl
+        import time
+        
+        # Sanitize features_df feature_id column
+        if hasattr(self, 'features_df') and self.features_df is not None and not self.features_df.is_empty():
+            # Check for null feature_ids
+            null_feature_ids = self.features_df.filter(pl.col("feature_id").is_null()).shape[0]
+            if null_feature_ids > 0:
+                self.logger.info(f"Sanitizing {null_feature_ids} null feature_id values with new integer IDs")
+                
+                # Find the maximum existing feature_id (convert strings to int if possible)
+                max_existing_id = 0
+                existing_ids = self.features_df.filter(pl.col("feature_id").is_not_null())["feature_id"].to_list()
+                for fid in existing_ids:
+                    try:
+                        int_id = int(fid)
+                        max_existing_id = max(max_existing_id, int_id)
+                    except (ValueError, TypeError):
+                        # Skip non-integer IDs
+                        pass
+                
+                # Generate new sequential integer IDs starting from max + timestamp offset
+                # Use timestamp to ensure uniqueness across different sanitization runs
+                base_id = max(max_existing_id + 1, int(time.time() * 1000000))  # Microsecond timestamp
+                new_int_ids = [str(base_id + i) for i in range(null_feature_ids)]
+                uid_index = 0
+                
+                # Create a list to store all feature_ids
+                feature_ids = []
+                for feature_id in self.features_df["feature_id"].to_list():
+                    if feature_id is None:
+                        feature_ids.append(new_int_ids[uid_index])
+                        uid_index += 1
+                    else:
+                        feature_ids.append(feature_id)
+                
+                # Update the DataFrame with sanitized feature_ids
+                self.features_df = self.features_df.with_columns(
+                    pl.Series("feature_id", feature_ids, dtype=pl.Utf8)
+                )
+                
+                self.logger.info(f"Successfully sanitized {null_feature_ids} feature_id values")
+        
+        # Sanitize consensus_df consensus_id column
+        if hasattr(self, 'consensus_df') and self.consensus_df is not None and not self.consensus_df.is_empty():
+            if "consensus_id" in self.consensus_df.columns:
+                null_consensus_ids = self.consensus_df.filter(pl.col("consensus_id").is_null()).shape[0]
+                if null_consensus_ids > 0:
+                    self.logger.info(f"Sanitizing {null_consensus_ids} null consensus_id values with new UIDs")
+                    
+                    # Generate new UIDs for null values using the same method as merge()
+                    new_uids = [str(uuid.uuid4()).replace('-', '')[:16] for _ in range(null_consensus_ids)]
+                    uid_index = 0
+                    
+                    # Create a list to store all consensus_ids
+                    consensus_ids = []
+                    for consensus_id in self.consensus_df["consensus_id"].to_list():
+                        if consensus_id is None:
+                            consensus_ids.append(new_uids[uid_index])
+                            uid_index += 1
+                        else:
+                            consensus_ids.append(consensus_id)
+                    
+                    # Update the DataFrame with sanitized consensus_ids
+                    self.consensus_df = self.consensus_df.with_columns(
+                        pl.Series("consensus_id", consensus_ids, dtype=pl.Utf8)
+                    )
+                    
+                    self.logger.info(f"Successfully sanitized {null_consensus_ids} consensus_id values")
+
     def __dir__(self):
         """
         Custom __dir__ implementation to hide internal methods starting with '_' 
@@ -627,16 +659,24 @@ class Study:
             'find_consensus',       # alias for merge  
             'integrate_chrom',      # alias for integrate
             'fill_chrom',           # alias for fill
-            'fill_chrom_single',    # alias for fill_single
             'filter_consensus',     # alias for consensus_filter
             'select_consensus',     # alias for consensus_select
             'filter_features',      # alias for features_filter
             'select_features',      # alias for features_select
             'consensus_find',       # alias for merge
+            # Backward compatibility for renamed methods
+            'set_folder',           # alias for set_study_folder
+            'set_source',           # alias for set_samples_source
+            'sample_color',         # alias for set_samples_color
+            'get_sample',           # alias for get_samples
+            'load_features',        # alias for _load_features
+            'store_history',        # alias for update_history
+            'sample_color_reset',   # alias for set_samples_color(by=None)
+            'reset_sample_color',   # alias for sample_color_reset
         }
         
         # Get all attributes from the class
-        all_attrs = set()
+        all_attrs: set[str] = set()
         
         # Add attributes from the class and all its bases
         for cls in self.__class__.__mro__:
@@ -895,8 +935,9 @@ class Study:
         tight_clusters_count = 0
         if consensus_df_len > 0:
             try:
+                from masster.study.merge import _count_tight_clusters
                 tight_clusters_count = _count_tight_clusters(self, mz_tol=0.04, rt_tol=0.3)
-            except Exception as e:
+            except Exception:
                 # If tight clusters calculation fails, just use 0
                 tight_clusters_count = 0
 
@@ -952,7 +993,6 @@ class Study:
 
         print(summary)
 
-
 if __name__ == "__main__":
     # This block is executed when the script is run directly
     pass

masster/study/study5_schema.json

@@ -327,6 +327,9 @@
       "formula": {
         "dtype": "pl.String"
       },
+      "iso": {
+        "dtype": "pl.Int64"
+      },
       "adduct": {
         "dtype": "pl.String"
       },
@@ -342,6 +345,9 @@
       "rt": {
         "dtype": "pl.Null"
       },
+      "quant_group": {
+        "dtype": "pl.Int64"
+      },
       "db_id": {
         "dtype": "pl.String"
       },
@@ -369,6 +375,9 @@
       },
       "score": {
         "dtype": "pl.Float64"
+      },
+      "iso": {
+        "dtype": "pl.Int64"
       }
     }
   }

{masster-0.4.22.dist-info → masster-0.5.1.dist-info}/METADATA

@@ -1,6 +1,6 @@
 Metadata-Version: 2.4
 Name: masster
-Version: 0.4.22
+Version: 0.5.1
 Summary: Mass spectrometry data analysis package
 Project-URL: homepage, https://github.com/zamboni-lab/masster
 Project-URL: repository, https://github.com/zamboni-lab/masster
@@ -686,6 +686,7 @@ Requires-Dist: bokeh>=3.7.3
 Requires-Dist: cmap>=0.6.2
 Requires-Dist: datashader>=0.18.1
 Requires-Dist: h5py>=3.14.0
+Requires-Dist: hdbscan>=0.8.40
 Requires-Dist: holoviews>=1.21.0
 Requires-Dist: hvplot>=0.11.3
 Requires-Dist: loguru>=0.7.3
@@ -701,6 +702,7 @@ Requires-Dist: pythonnet>=3.0.0
 Requires-Dist: scikit-learn>=1.7.1
 Requires-Dist: scipy>=1.12.0
 Requires-Dist: tqdm>=4.65.0
+Requires-Dist: umap-learn>=0.5.9.post2
 Provides-Extra: dev
 Requires-Dist: bandit>=1.7.0; extra == 'dev'
 Requires-Dist: black>=23.0.0; extra == 'dev'
@@ -726,12 +728,13 @@ Description-Content-Type: text/markdown
 
 # MASSter
 
-**MASSter** is a comprehensive Python package for mass spectrometry data analysis, designed for metabolomics and LC-MS data processing. It provides tools for feature detection, alignment, consensus building, and interactive visualization of mass spectrometry datasets. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data. 
+**MASSter** is a Python package for the analysis of mass spectrometry data, tailored for the purpose of metabolomics and LC-MS data processing. It is designed to deal with DDA, and hides functionalities for DIA and ZTScan DIA data. The sample-centric feature detection uses OpenMS. All other functionalities for e.g. centroiding, RT alignment, adduct and isotopomer detection, merging of multiple samples, gap-filling, quantification, etc. were redesigned and engineered to maximize scalability (tested with 3000 LC-MS), speed, quality, and results.
 
 This is a poorly documented, stable branch of the development codebase in use in the Zamboni lab. 
 
-Some of the core processing functions are derived from OpenMS. We use the same nomenclature and refer to their documentation for an explanation of the parameters. To a large extent, however, you should be able to use the defaults (=no parameters) when calling processing steps.
+## Prerequisites
 
+**MASSter** reads raw (Thermo), wiff (SCIEX), or mzML data. It's recommended to provide raw, profile data.
 
 ## Installation
 
@@ -739,20 +742,60 @@ Some of the core processing functions are derived from OpenMS. We use the same n
 pip install masster
 ```
 
-### Basic Workflow for analyzing LC-MS study with 2-... samples
+## Basic usage
+### Quick start: use the wizard
+
+```python
+import masster
+masster.wizard.execute(
+    source=r'..\..\folder_with_raw_data',
+    folder=r'..\..folder_to_store_results'
+    )
+```
 
+This will run a wizard that should perform all key steps and save the results to the `folder`.
+
+### Basic workflow for analyzing a single sample
 ```python
 import masster
+sample = masster.Sample(filename='...') # full path to a *.raw, *.wiff, or *.mzML file
+# process
+sample.find_features(chrom_fwhm=0.5, noise=50) # for orbitrap data, set noise to 1e5
+sample.find_adducts()
+sample.find_ms2()
+
+# access data
+sample.features_df
+
+# save results
+sample.save() # stores to *.sample5, our custom hdf5 format
+sample.export_mgf()
+
+# some plots
+sample.plot_bpc()
+sample.plot_tic()
+sample.plot_2d()
+sample.plot_features_stats()
+
+# explore methods
+dir(study)
+```
+
+### Basic Workflow for analyzing LC-MS study with 2-... samples
 
+```python
+import masster
 # Initialize the Study object with the default folder
-study = masster.Study(default_folder=r'D:\...\mylcms')
+study = masster.Study(folder=r'D:\...\mylcms')
 
 # Load data from folder with raw data, here: WIFF
 study.add(r'D:\...\...\...\*.wiff')
 
 # Perform retention time correction
-study.align(rt_max_diff=2.0)
+study.align(rt_tol=2.0)
 study.plot_alignment()
+study.plot_bpc()
+study.plot_rt_correction()
 
 # Find consensus features
 study.merge(min_samples=3)
@@ -772,18 +815,15 @@ study.export_parquet()
 
 # Save the study to .study5
 study.save()
-```
-
-## Requirements
 
-- Python ≥ 3.11
-- Key dependencies: pandas, polars, numpy, scipy, matplotlib, bokeh, holoviews, panel
-- See `pyproject.toml` for complete dependency list
+# Some of the plots...
+study.plot_samples_pca()
+study.plot_samples_umap()
+study.plot_samples_2d()
+```
 
 ## License
-
 GNU Affero General Public License v3
 
 ## Citation
-
 If you use Masster in your research, please cite this repository.