ms-mint 0.2.4__tar.gz → 0.3.0__tar.gz

{ms-mint-0.2.4/ms_mint.egg-info → ms-mint-0.3.0}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ms-mint
-Version: 0.2.4
+Version: 0.3.0
 Summary: Metabolomics Integrator (Mint)
 Home-page: https://github.com/LewisResearchGroup/ms-mint
 Author: Soren Wacker
@@ -16,19 +16,28 @@ License-File: LICENSE
 ![](https://github.com/LewisResearchGroup/ms-mint/blob/develop/images/coverage.svg)
 [![CodeQL](https://github.com/lewisresearchgroup/ms-mint/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/lewisresearchgroup/ms-mint/actions/workflows/codeql-analysis.yml)
 
-# Wecome to ms-mint 
+# Wecome to ms-mint
 
 ## A Python library for targeted metabolomics
 The `ms-mint` library is a tool designed to assist with targeted metabolomics studies, which involves the systematic analysis of small chemical compounds called metabolites that are present in biological samples. These metabolites can provide valuable information about the state of an organism, including indicators of disease or other physiological changes. In order to perform a targeted metabolomics study, researchers typically use liquid chromatography-mass spectrometry (LCMS) to identify and quantify specific metabolites of interest.
 
 The `ms-mint` library includes a range of functions for processing LCMS data from targeted metabolomics experiments, and it is particularly well-suited for handling large amounts of data (10,000+ files). To use `ms-mint`, you provide it with a target list of the specific metabolites you want to analyze, as well as the names of the mass spectrometry files containing the data. ms-mint then extracts peak intensities and other relevant information from the data, allowing you to gain insights into the concentrations and profiles of the metabolites in your samples. This information can be used to identify biomarkers, which are indicators of disease or other physiological changes that can be used in the development of diagnostic tests or other medical applications.
 
+## Installation
+
+    pip install ms-mint
+
+
 ## Documentation
 The code documentation can be accessed [here](https://lewisresearchgroup.github.io/ms-mint/readme.html).
 
 ## ms-mint application with graphical user iterface (GUI)
 MINT has been split into the Python library and the app. This repository contains the Python library. For the app follow [this link](https://github.com/LewisResearchGroup/ms-mint-app).
 
+## Publications that used ms-mint
+1. Brown K, Thomson CA, Wacker S, Drikic M, Groves R, Fan V, et al. [Microbiota alters the metabolome in an age- and sex- dependent manner in mice.](https://pubmed.ncbi.nlm.nih.gov/36906623/) Nat Commun. 2023;14: 1348.
+
+---
 ## Contributions
 All contributions, bug reports, code reviews, bug fixes, documentation improvements, enhancements, and ideas are welcome.
 Before you modify the code please reach out to us using the [issues](https://github.com/LewisResearchGroup/ms-mint/issues) page.
@@ -36,8 +45,6 @@ Before you modify the code please reach out to us using the [issues](https://git
 ## Code standards
 The project follows PEP8 standard and uses Black and Flake8 to ensure a consistent code format throughout the project.
 
----
-
 ## Usage
 
 To use the main class of the ms-mint library, you can import it into your code with the following command:
@@ -129,7 +136,7 @@ If you only have retention time (Rt) values for your targets, or if the Rt value
 
 To use the `mint.opt.rt_min_max()` function, you will need to provide it with a list of retention times for your targets and the names of the mass spectrometry files containing your data. The function will then search through the data to find the optimal `rt_min` and `rt_max` values, which you can use to refine your analysis. You can then use these optimized values in conjunction with the other functions and methods of the `Mint` class to process and analyze your data.
 
-![](notebooks/peak-shapes-before-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-before-opt.png)
 
 Now, we can run the peak optimization with:
 
@@ -146,7 +153,7 @@ If you do not provide a list of peak_labels to the `mint.opt.rt_min_max()` funct
 
 After running the optimization, it is a good idea to perform a manual fine-tuning of the `rt_min` and `rt_max` values, especially for complicated peaks (peaks with multiple components, noisy peaks, etc.). You can use the `mint.plot.peak_shapes()` function to visualize the peak shapes and identify any areas that may require further attention.
     
-![](notebooks/optimize-rt_min_max.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/optimize-rt_min_max.png)
 
 The black lines indicates the average intensity across all files used for the optimization. The orange dotted lines show the shape of the gaussian function used to weight the mean intensities for peak selection. The orange horizontal lines indicate the peak width and the blue `x`s show the identified peak maxima. The green shaded areas show the Rt ranges which were selected by the algorithm.
 
@@ -155,7 +162,7 @@ Then we apply the changes and plot the new peak shapes:
     mint.run()
     mint.plot.peak_shapes(col_wrap=3)
 
-![](notebooks/peak-shapes-after-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-after-opt.png)
 
 As you can see, the shapes of Xanthine, Succinate, Citrulline look much better.
 
@@ -165,7 +172,7 @@ The `Mint` class has a few convenient methods to visualize and explore the proce
 
 ## Plot peak shapes
 
-![](notebooks/peak-shapes-after-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-after-opt.png)
 
     mint.plot.peak_shapes(col_wrap = 3)
 
@@ -200,7 +207,7 @@ Before clustering the data can be transformed and scaled. By default `log2p1(x)
         cmap=None  # Name of a matplotlib color map                
     )
 
-![](notebooks/hierarchical_clustering.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/hierarchical_clustering.png)
 
 ## Principal Components Analysis
 
@@ -214,7 +221,7 @@ After running the PCA the results can be plotted with:
     
     mint.pca.plot.pairplot(n_components=5, interactive=False)
     
-![](notebooks/pca-pairplot.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/pca-pairplot.png)
 
 ## FAQ
 ### What is a target list

{ms-mint-0.2.4 → ms-mint-0.3.0}/README.md

@@ -2,19 +2,28 @@
 ![](https://github.com/LewisResearchGroup/ms-mint/blob/develop/images/coverage.svg)
 [![CodeQL](https://github.com/lewisresearchgroup/ms-mint/actions/workflows/codeql-analysis.yml/badge.svg)](https://github.com/lewisresearchgroup/ms-mint/actions/workflows/codeql-analysis.yml)
 
-# Wecome to ms-mint 
+# Wecome to ms-mint
 
 ## A Python library for targeted metabolomics
 The `ms-mint` library is a tool designed to assist with targeted metabolomics studies, which involves the systematic analysis of small chemical compounds called metabolites that are present in biological samples. These metabolites can provide valuable information about the state of an organism, including indicators of disease or other physiological changes. In order to perform a targeted metabolomics study, researchers typically use liquid chromatography-mass spectrometry (LCMS) to identify and quantify specific metabolites of interest.
 
 The `ms-mint` library includes a range of functions for processing LCMS data from targeted metabolomics experiments, and it is particularly well-suited for handling large amounts of data (10,000+ files). To use `ms-mint`, you provide it with a target list of the specific metabolites you want to analyze, as well as the names of the mass spectrometry files containing the data. ms-mint then extracts peak intensities and other relevant information from the data, allowing you to gain insights into the concentrations and profiles of the metabolites in your samples. This information can be used to identify biomarkers, which are indicators of disease or other physiological changes that can be used in the development of diagnostic tests or other medical applications.
 
+## Installation
+
+    pip install ms-mint
+
+
 ## Documentation
 The code documentation can be accessed [here](https://lewisresearchgroup.github.io/ms-mint/readme.html).
 
 ## ms-mint application with graphical user iterface (GUI)
 MINT has been split into the Python library and the app. This repository contains the Python library. For the app follow [this link](https://github.com/LewisResearchGroup/ms-mint-app).
 
+## Publications that used ms-mint
+1. Brown K, Thomson CA, Wacker S, Drikic M, Groves R, Fan V, et al. [Microbiota alters the metabolome in an age- and sex- dependent manner in mice.](https://pubmed.ncbi.nlm.nih.gov/36906623/) Nat Commun. 2023;14: 1348.
+
+---
 ## Contributions
 All contributions, bug reports, code reviews, bug fixes, documentation improvements, enhancements, and ideas are welcome.
 Before you modify the code please reach out to us using the [issues](https://github.com/LewisResearchGroup/ms-mint/issues) page.
@@ -22,8 +31,6 @@ Before you modify the code please reach out to us using the [issues](https://git
 ## Code standards
 The project follows PEP8 standard and uses Black and Flake8 to ensure a consistent code format throughout the project.
 
----
-
 ## Usage
 
 To use the main class of the ms-mint library, you can import it into your code with the following command:
@@ -115,7 +122,7 @@ If you only have retention time (Rt) values for your targets, or if the Rt value
 
 To use the `mint.opt.rt_min_max()` function, you will need to provide it with a list of retention times for your targets and the names of the mass spectrometry files containing your data. The function will then search through the data to find the optimal `rt_min` and `rt_max` values, which you can use to refine your analysis. You can then use these optimized values in conjunction with the other functions and methods of the `Mint` class to process and analyze your data.
 
-![](notebooks/peak-shapes-before-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-before-opt.png)
 
 Now, we can run the peak optimization with:
 
@@ -132,7 +139,7 @@ If you do not provide a list of peak_labels to the `mint.opt.rt_min_max()` funct
 
 After running the optimization, it is a good idea to perform a manual fine-tuning of the `rt_min` and `rt_max` values, especially for complicated peaks (peaks with multiple components, noisy peaks, etc.). You can use the `mint.plot.peak_shapes()` function to visualize the peak shapes and identify any areas that may require further attention.
     
-![](notebooks/optimize-rt_min_max.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/optimize-rt_min_max.png)
 
 The black lines indicates the average intensity across all files used for the optimization. The orange dotted lines show the shape of the gaussian function used to weight the mean intensities for peak selection. The orange horizontal lines indicate the peak width and the blue `x`s show the identified peak maxima. The green shaded areas show the Rt ranges which were selected by the algorithm.
 
@@ -141,7 +148,7 @@ Then we apply the changes and plot the new peak shapes:
     mint.run()
     mint.plot.peak_shapes(col_wrap=3)
 
-![](notebooks/peak-shapes-after-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-after-opt.png)
 
 As you can see, the shapes of Xanthine, Succinate, Citrulline look much better.
 
@@ -151,7 +158,7 @@ The `Mint` class has a few convenient methods to visualize and explore the proce
 
 ## Plot peak shapes
 
-![](notebooks/peak-shapes-after-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-after-opt.png)
 
     mint.plot.peak_shapes(col_wrap = 3)
 
@@ -186,7 +193,7 @@ Before clustering the data can be transformed and scaled. By default `log2p1(x)
         cmap=None  # Name of a matplotlib color map                
     )
 
-![](notebooks/hierarchical_clustering.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/hierarchical_clustering.png)
 
 ## Principal Components Analysis
 
@@ -200,7 +207,7 @@ After running the PCA the results can be plotted with:
     
     mint.pca.plot.pairplot(n_components=5, interactive=False)
     
-![](notebooks/pca-pairplot.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/pca-pairplot.png)
 
 ## FAQ
 ### What is a target list

ms-mint-0.2.4/ms_mint/chromatogram.py → ms-mint-0.3.0/ms_mint/Chromatogram.py

@@ -6,31 +6,48 @@ from matplotlib import pyplot as plt
 
 from .tools import find_peaks_in_timeseries, gaussian, mz_mean_width_to_min_max
 from .io import ms_file_to_df
-from .filters import Resampler, Smoother, GaussFilter
+from .filters import Filter, Resampler, Smoother, GaussFilter
 from .matplotlib_tools import plot_peaks
+from .processing import get_chromatogram_from_ms_file
+
+from typing import Optional, Union, List, Any
 
 
 class Chromatogram:
     def __init__(
-        self, scan_times=None, intensities=None, filters=None, expected_rt=None
+        self,
+        scan_times: Optional[Union[List[float], np.ndarray]] = None,
+        intensities: Optional[Union[List[float], np.ndarray]] = None,
+        filters: Optional[List[Filter]] = None,
+        expected_rt: Optional[float] = None
     ):
-        self.t = np.array([0])
-        self.x = np.array([0])
+        """
+        Initialize a Chromatogram object.
+
+        :param scan_times: Array-like object containing the scan times.
+        :param intensities: Array-like object containing the intensities.
+        :param filters: List of filters to be applied.
+        :param expected_rt: Expected retention time.
+        """
+        # Initialize empty arrays for scan_times and intensities
+        # Initialize scan_times and intensities as empty lists or arrays
+        self.t = np.array([]) if scan_times is None or 0 in scan_times else np.array([0])
+        self.x = np.array([]) if intensities is None or 0 in scan_times else np.array([0])
+
+        # Update scan_times and intensities if provided
         if scan_times is not None:
             self.t = np.append(self.t, scan_times)
         if intensities is not None:
             self.x = np.append(self.x, intensities)
-        self.noise_level = None
-        if filters is None:
-            self.filters = [Resampler(), GaussFilter(), Smoother()]
-        else:
-            self.filters = filters
-        self.peaks = None
-        self.selected_peak_ndxs = None
-        if expected_rt is None and scan_times is not None:
-            expected_rt = max(scan_times) // 2
+
+        # Initialize other attributes
+        self.noise_level: Optional[float] = None
+        self.filters: List[Any] = filters or [Resampler(), GaussFilter(), Smoother()]
+        self.peaks: Optional[pd.DataFrame] = None
+        self.selected_peak_ndxs: Optional[List[int]] = None
         self.expected_rt = expected_rt
-        self.weights = None
+        self.weights: Optional[Union[List[float], np.ndarray]] = None
+
 
     def from_file(self, fn, mz_mean, mz_width=10, expected_rt=None):
         chrom = get_chromatogram_from_ms_file(fn, mz_mean=mz_mean, mz_width=mz_width)
@@ -47,14 +64,15 @@ class Chromatogram:
         for filt in self.filters:
             self.t, self.x = filt.transform(self.t, self.x)
 
-    def find_peaks(self, prominence=None, rel_height=0.9):
+    def find_peaks(self, prominence=None, rel_height=0.9, **kwargs):
         self.estimate_noise_level()
         if prominence is None:
-            prominence = self.noise_level * 3
+            prominence = self.noise_level * 5
         self.peaks = find_peaks_in_timeseries(
             self.data.intensity,
             prominence=prominence,
             rel_height=rel_height,
+            **kwargs
         )
 
     def optimise_peak_times_with_diff(self, rolling_window=20, plot=False):
@@ -153,15 +171,3 @@ class Chromatogram:
         )
         return fig
 
-
-def get_chromatogram_from_ms_file(ms_file, mz_mean, mz_width=10):
-    df = ms_file_to_df(ms_file)
-    chrom = extract_chromatogram_from_ms1(df, mz_mean, mz_width=mz_width)
-    return chrom
-
-
-def extract_chromatogram_from_ms1(ms1, mz_mean, mz_width=10):
-    mz_min, mz_max = mz_mean_width_to_min_max(mz_mean, mz_width)
-    chrom = ms1[(ms1["mz"] >= mz_min) & (ms1["mz"] <= mz_max)].copy()
-    chrom = chrom.groupby("scan_time", as_index=False).sum(numeric_only=True)
-    return chrom.set_index("scan_time")["intensity"]

{ms-mint-0.2.4 → ms-mint-0.3.0}/ms_mint/Mint.py

@@ -11,20 +11,21 @@ from multiprocessing import Pool, Manager, cpu_count
 from glob import glob
 
 from .standards import MINT_RESULTS_COLUMNS, TARGETS_COLUMNS, DEPRECATED_LABELS
-from .processing import process_ms1_files_in_parallel
+from .processing import process_ms1_files_in_parallel, extract_chromatogram_from_ms1
 from .io import export_to_excel, ms_file_to_df
-from .targets import read_targets, check_targets, standardize_targets, TargetOptimizer
+from .TargetOptimizer import TargetOptimizer
+from .targets import read_targets, check_targets, standardize_targets
 from .tools import (
     is_ms_file,
     get_ms_files_from_results,
     get_targets_from_results,
     scale_dataframe,
+    init_metadata,
+    fn_to_label
 )
 from .pca import PrincipalComponentsAnalyser
-from .plotting import MintPlotter
-
-# from .filter import Resampler
-from .chromatogram import Chromatogram, extract_chromatogram_from_ms1
+from .MintPlotter import MintPlotter
+from .Chromatogram import Chromatogram
 
 import ms_mint
 
@@ -33,6 +34,7 @@ from tqdm import tqdm
 from typing import Callable
 from functools import lru_cache
 
+METADATA_DEFAUT_FN = 'metadata.parquet'
 
 class Mint(object):
     """
@@ -44,6 +46,8 @@ class Mint(object):
     :param progress_callback: A callback for a progress bar.
     :type progress_callback: Callable[]
 
+    :parm wdir: Working directory
+    :type wdir: str
     """
 
     def __init__(
@@ -51,18 +55,21 @@ class Mint(object):
         verbose: bool = False,
         progress_callback: Callable = None,
         time_unit: str = "s",
+        wdir: str = None
     ):
         self.verbose = verbose
         self._version = ms_mint.__version__
+        print("Mint version:", self.version, "\n")
         self.progress_callback = progress_callback
         self.reset()
-        if self.verbose:
-            print("Mint Version:", self.version, "\n")
         self.plot = MintPlotter(mint=self)
         self.opt = TargetOptimizer(mint=self)
         self.pca = PrincipalComponentsAnalyser(self)
         self.tqdm = tqdm
-        self.meta = None
+
+        # Setup working directory as pathlib.Path
+        self.wdir = os.getcwd() if wdir is None else wdir
+        self.wdir = P(self.wdir)
 
     @property
     def version(self):
@@ -90,6 +97,7 @@ class Mint(object):
         self.runtime = None
         self._status = "waiting"
         self._messages = []
+        self.meta = init_metadata()
         return self
 
     def clear_targets(self):
@@ -200,7 +208,6 @@ class Mint(object):
     def _run_parallel(
         self, nthreads=1, mode="standard", maxtasksperchild=None, fn=None
     ):
-        print(f"maxtasksperchild: {maxtasksperchild}")
         pool = Pool(processes=nthreads, maxtasksperchild=maxtasksperchild)
         m = Manager()
         q = m.Queue()
@@ -274,6 +281,7 @@ class Mint(object):
         self._files = list_of_files
         if self.verbose:
             print("Set files to:\n" + "\n".join(self.ms_files) + "\n")
+        self.meta = self.meta.reindex([fn_to_label(fn) for fn in list_of_files])
 
     @property
     def n_files(self):
@@ -373,7 +381,7 @@ class Mint(object):
     def results(self, df):
         self._results = df
 
-    def crosstab(self, col_name="peak_max", apply=None, scaler=None):
+    def crosstab(self, values: str = "peak_max", index: str = None, column: str = None, aggfunc: str = 'mean', apply: Callable = None, scaler: Callable = None):
         """
         Create condensed representation of the results.
         More specifically, a cross-table with filenames as index and target labels.
@@ -384,12 +392,23 @@ class Mint(object):
 
         cells of the returned table.
         """
+        
+        df_meta = pd.merge(self.meta, self.results, left_index=True, right_on='ms_file_label')
+
+        if index is None:
+            index = 'ms_file_label'
+        if column is None:
+            column = 'peak_label'
+        if values is None:
+            values = 'peak_area_top3'
+
         df = pd.crosstab(
-            self.results.ms_file,
-            self.results.peak_label,
-            self.results[col_name],
-            aggfunc=sum,
+            df_meta[index],
+            df_meta[column],
+            df_meta[values],
+            aggfunc=aggfunc,
         ).astype(np.float64)
+
         if apply:
             df = df.apply(apply)
         if scaler:
@@ -462,6 +481,11 @@ class Mint(object):
                 results = pd.read_parquet(fn)
         else:
             results = pd.read_csv(fn)
+
+        # Add file labels if not present already    
+        if 'ms_file_label' not in results.columns:
+            results['ms_file_label'] = [fn_to_label(fn) for fn in results.ms_file]
+
         self.results = results.rename(columns=DEPRECATED_LABELS)
         self.digest_results()
         return self
@@ -470,35 +494,47 @@ class Mint(object):
         self.ms_files = get_ms_files_from_results(self.results)
         self.targets = get_targets_from_results(self.results)
 
-    @lru_cache(1)
-    def get_chromatograms(self, fns=None, peak_label=None, **kwargs):
+
+    def get_chromatograms(self, fns=None, peak_labels=None, filters=None, **kwargs):
         if fns is None:
             fns = self.ms_files
+        if peak_labels is None:
+            peak_labels = self.peak_labels
+        return self._get_chromatograms(fns=tuple(fns), peak_labels=tuple(peak_labels), 
+                                       filters=tuple(filters) if filters is not None else None, **kwargs)
+
+    @lru_cache(1)
+    def _get_chromatograms(self, fns=None, peak_labels=None, filters=None, **kwargs):
 
         if isinstance(fns, tuple):
-            fns = list(fns)
+            fns = list(fns)     
 
         if not isinstance(fns, list):
             fns = [fns]
 
-        if peak_label is None:
-            peak_label = self.peak_labels
+        labels = [fn_to_label(fn) for fn in fns]
+
+        # Need to get the actual file names with get_chromatogramsath
+        # in case only ms_file_labels are provided
+        fns = [fn for fn in self.ms_files if fn_to_label(fn) in labels]
 
         data = []
 
-        for fn in self.tqdm(fns):
+        for fn in self.tqdm(fns, desc="Loading chromatograms"):
             df = ms_file_to_df(fn)
-            for label in peak_label:
+            for label in peak_labels:
                 mz_mean, mz_width, rt_min, rt_max = self.get_target_params(label)
                 chrom_raw = extract_chromatogram_from_ms1(
                     df, mz_mean=mz_mean, mz_width=mz_width
                 ).to_frame()
                 if len(chrom_raw) == 0:
                     continue
-                chrom = Chromatogram(chrom_raw.index, chrom_raw.values)
-                chrom.apply_filter()
+                chrom = Chromatogram(chrom_raw.index, chrom_raw.values, filters=filters, **kwargs)
+                if filters is not None:
+                    chrom.apply_filters()
                 chrom_data = chrom.data
                 chrom_data["ms_file"] = fn
+                chrom_data["ms_file_label"] = fn_to_label(fn)
                 chrom_data["peak_label"] = label
                 chrom_data["rt_min"] = rt_min
                 chrom_data["rt_max"] = rt_max
@@ -508,3 +544,23 @@ class Mint(object):
 
         data["ms_file"] = data["ms_file"].apply(lambda x: P(x).with_suffix("").name)
         return data
+
+    def load_metadata(self, fn=None):
+        if fn is None:
+            fn = self.wdir/METADATA_DEFAUT_FN
+        if str(fn).endswith('.csv'):
+            self.meta = pd.read_csv(fn, index_col=0)
+        elif str(fn).endswith('.parquet'):
+            self.meta = pd.read_parquet(fn)
+        if 'ms_file_label' in self.meta.columns:
+            self.meta = self.meta.set_index('ms_file_label')
+        return self
+
+    def save_metadata(self, fn=None):
+        if fn is None:
+            fn = self.wdir/METADATA_DEFAUT_FN
+        if str(fn).endswith('.csv'):
+            self.meta.to_csv(fn, na_filter=False)
+        elif str(fn).endswith('.parquet'):
+            self.meta.to_parquet(fn)
+        return self

ms-mint-0.2.4/ms_mint/plotting.py → ms-mint-0.3.0/ms_mint/MintPlotter.py

@@ -147,6 +147,7 @@ class MintPlotter:
         else:
             self.mint.clustered = data.iloc[ndx_y, ndx_x]
         return fig
+    
 
     def peak_shapes(self, fns=None, peak_labels=None, interactive=False, **kwargs):
         """Plot peak shapes.
@@ -263,7 +264,7 @@ class MintPlotter:
             plt.title(f'{P(fn).with_suffix("").name}\n{peak_label}')
         return fig
 
-    def chromatogram(self, fns=None, peak_labels=None, interactive=False, **kwargs):
+    def chromatogram(self, fns=None, peak_labels=None, interactive=False, filters=None, **kwargs):
         """Plot the chromatogram extracted from one or more files.
 
         :param fns: File names to extract chromatogram from.
@@ -294,7 +295,7 @@ class MintPlotter:
         if peak_labels is not None:
             peak_labels = tuple(peak_labels)
 
-        data = self.mint.get_chromatograms(fns=fns, peak_labels=peak_labels)
+        data = self.mint.get_chromatograms(fns=fns, peak_labels=peak_labels, filters=filters)
 
         if not interactive:
             params = dict(
@@ -305,7 +306,7 @@ class MintPlotter:
                 col_order=peak_labels,
                 height=1.5,
                 aspect=5,
-                hue="ms_file",
+                hue="ms_file_label",
                 facet_kws=dict(sharey=False),
                 marker=".",
                 linewidth=0,
@@ -331,7 +332,7 @@ class MintPlotter:
                 x="scan_time",
                 y="intensity",
                 facet_col="peak_label",
-                color="ms_file",
+                color="ms_file_label",
                 height=700,
                 facet_col_wrap=1,
             )