ms-mint 0.3.1__tar.gz → 0.3.2__tar.gz

{ms-mint-0.3.1/ms_mint.egg-info → ms-mint-0.3.2}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ms-mint
-Version: 0.3.1
+Version: 0.3.2
 Summary: Metabolomics Integrator (Mint)
 Home-page: https://github.com/LewisResearchGroup/ms-mint
 Author: Soren Wacker
@@ -15,6 +15,8 @@ License-File: LICENSE
 [![Python package](https://github.com/LewisResearchGroup/ms-mint/actions/workflows/pythonpackage.yml/badge.svg)](https://github.com/LewisResearchGroup/ms-mint/actions/workflows/pythonpackage.yml)
 ![](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)
+![PyPI](https://img.shields.io/pypi/v/ms-mint?label=pypi%20package)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/ms-mint)
 
 # Wecome to ms-mint
 
@@ -136,7 +138,7 @@ 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.
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-before-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/peak-shapes-before-opt.png)
 
 Now, we can run the peak optimization with:
 
@@ -153,7 +155,7 @@ 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.
     
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/optimize-rt_min_max.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/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.
 
@@ -162,7 +164,7 @@ Then we apply the changes and plot the new peak shapes:
     mint.run()
     mint.plot.peak_shapes(col_wrap=3)
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-after-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/peak-shapes-after-opt.png)
 
 As you can see, the shapes of Xanthine, Succinate, Citrulline look much better.
 
@@ -172,7 +174,7 @@ The `Mint` class has a few convenient methods to visualize and explore the proce
 
 ## Plot peak shapes
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-after-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/peak-shapes-after-opt.png)
 
     mint.plot.peak_shapes(col_wrap = 3)
 
@@ -207,7 +209,7 @@ Before clustering the data can be transformed and scaled. By default `log2p1(x)
         cmap=None  # Name of a matplotlib color map                
     )
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/hierarchical_clustering.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/hierarchical_clustering.png)
 
 ## Principal Components Analysis
 
@@ -221,7 +223,7 @@ After running the PCA the results can be plotted with:
     
     mint.pca.plot.pairplot(n_components=5, interactive=False)
     
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/pca-pairplot.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/pca-pairplot.png)
 
 ## FAQ
 ### What is a target list

{ms-mint-0.3.1 → ms-mint-0.3.2}/README.md

@@ -1,6 +1,8 @@
 [![Python package](https://github.com/LewisResearchGroup/ms-mint/actions/workflows/pythonpackage.yml/badge.svg)](https://github.com/LewisResearchGroup/ms-mint/actions/workflows/pythonpackage.yml)
 ![](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)
+![PyPI](https://img.shields.io/pypi/v/ms-mint?label=pypi%20package)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/ms-mint)
 
 # Wecome to ms-mint
 
@@ -122,7 +124,7 @@ 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.
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-before-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/peak-shapes-before-opt.png)
 
 Now, we can run the peak optimization with:
 
@@ -139,7 +141,7 @@ 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.
     
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/optimize-rt_min_max.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/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.
 
@@ -148,7 +150,7 @@ Then we apply the changes and plot the new peak shapes:
     mint.run()
     mint.plot.peak_shapes(col_wrap=3)
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-after-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/peak-shapes-after-opt.png)
 
 As you can see, the shapes of Xanthine, Succinate, Citrulline look much better.
 
@@ -158,7 +160,7 @@ The `Mint` class has a few convenient methods to visualize and explore the proce
 
 ## Plot peak shapes
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-after-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/peak-shapes-after-opt.png)
 
     mint.plot.peak_shapes(col_wrap = 3)
 
@@ -193,7 +195,7 @@ Before clustering the data can be transformed and scaled. By default `log2p1(x)
         cmap=None  # Name of a matplotlib color map                
     )
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/hierarchical_clustering.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/hierarchical_clustering.png)
 
 ## Principal Components Analysis
 
@@ -207,7 +209,7 @@ After running the PCA the results can be plotted with:
     
     mint.pca.plot.pairplot(n_components=5, interactive=False)
     
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/pca-pairplot.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/pca-pairplot.png)
 
 ## FAQ
 ### What is a target list

{ms-mint-0.3.1 → ms-mint-0.3.2}/ms_mint/MintPlotter.py

@@ -133,11 +133,11 @@ class MintPlotter:
         if len(self.mint.results) > 0:
             if not interactive:
                 return plot_peak_shapes(
-                    self.mint.results, fns=fns, peak_labels=peak_labels, **kwargs
+                    self.mint.results, mint_metadata=self.mint.meta, fns=fns, peak_labels=peak_labels, **kwargs
                 )
             else:
                 return plotly_peak_shapes(
-                    self.mint.results, fns=fns, peak_labels=peak_labels, **kwargs
+                    self.mint.results, mint_metadata=self.mint.meta, fns=fns, peak_labels=peak_labels, **kwargs
                 )
 
     def heatmap(

{ms-mint-0.3.1 → ms-mint-0.3.2}/ms_mint/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-07-14T14:57:31-0600",
+ "date": "2023-08-18T12:58:02-0600",
  "dirty": false,
  "error": null,
- "full-revisionid": "f07adddea947021c45a6e0b9160b1734655561e7",
- "version": "v0.3.1"
+ "full-revisionid": "2563246318a0e00988500da34daed80721f81b98",
+ "version": "v0.3.2"
 }
 '''  # END VERSION_JSON
 

{ms-mint-0.3.1 → ms-mint-0.3.2}/ms_mint/matplotlib_tools.py

@@ -130,17 +130,19 @@ def hierarchical_clustering(
 
 def plot_peak_shapes(
     mint_results,
+    mint_metadata=None,
     fns=None,
     peak_labels=None,
     height=3,
     aspect=1.5,
     legend=False,
     col_wrap=4,
-    hue="ms_file",
+    hue="ms_file_label",
     title=None,
     dpi=None,
     sharex=False,
     sharey=False,
+    kind='line',
     **kwargs,
 ):
     """
@@ -148,6 +150,8 @@ def plot_peak_shapes(
 
     :param mint_results: DataFrame in Mint results format.
     :type mint_results: pandas.DataFrame
+    :param mint_metadata: DataFrame in Mint metadata format.
+    :type mint_metadata: pandas.DataFrame
     :param fns: Filenames to include, defaults to None
     :type fns: list, optional
     :param peak_labels: Peak-labels to include, defaults to None
@@ -170,6 +174,8 @@ def plot_peak_shapes(
     :type sharex: bool, optional
     :param sharey: Whether or not to share y-axis range between subplots, defaults to False
     :type sharey: bool, optional
+    :param kind: Kind of seaborn relplot
+    :type kind: str, optional
     :return: Generated figure object.
     :rtype: matplotlib.pyplot.Figure
     """
@@ -197,7 +203,7 @@ def plot_peak_shapes(
         ].iterrows():
             peak_rt = [float(i) for i in row.peak_shape_rt.split(",")]
             peak_int = [float(i) for i in row.peak_shape_int.split(",")]
-            ms_file = row.ms_file
+            ms_file_label = row.ms_file_label
             mz = row.mz_mean
             rt = row.rt
 
@@ -205,7 +211,7 @@ def plot_peak_shapes(
                 {
                     "Scan time [s]": peak_rt,
                     "Intensity": peak_int,
-                    "ms_file": ms_file,
+                    "ms_file_label": ms_file_label,
                     "peak_label": peak_label + f"\nm/z={mz:.3f}",
                     "Expected Scan time [s]": rt,
                 }
@@ -214,13 +220,17 @@ def plot_peak_shapes(
 
     df = pd.concat(dfs).reset_index(drop=True)
 
+    # Add metadata
+    if mint_metadata is not None:
+        df = pd.merge(df, mint_metadata, left_on='ms_file_label', right_index=True)
+
     g = sns.relplot(
         data=df,
         x="Scan time [s]",
         y="Intensity",
         hue=hue,
         col="peak_label",
-        kind="line",
+        kind=kind,
         col_wrap=col_wrap,
         height=height,
         aspect=aspect,

{ms-mint-0.3.1 → ms-mint-0.3.2}/ms_mint/plotly_tools.py

@@ -1,6 +1,7 @@
 import logging
 
 import numpy as np
+import pandas as pd
 import colorlover as cl
 
 import plotly.graph_objects as go
@@ -222,6 +223,8 @@ def plotly_heatmap(
 
 def plotly_peak_shapes(
     mint_results,
+    mint_metadata=None,
+    color='ms_file_label',  # Add the new argument for specifying color column
     fns=None,
     col_wrap=1,
     peak_labels=None,
@@ -229,52 +232,90 @@ def plotly_peak_shapes(
     verbose=False,
     legend_orientation="v",
     call_show=False,
+    palette='Plasma',
 ):
-    """
-    Returns a plotly multiplost of all peak_shapes in mint.results
-    grouped by peak_label.
+    """ 
+    Plot peak shapes of mint results.
+
+    :param mint_results: DataFrame in Mint results format.
+    :type mint_results: pandas.DataFrame
+    :param mint_metadata: DataFrame in Mint metadata format, defaults to None.
+    :type mint_metadata: pandas.DataFrame, optional
+    :param color: Column name determining color-coding of plots, defaults to 'ms_file_label'.
+    :type color: str, optional
+    :param fns: Filenames to include, defaults to None.
+    :type fns: list, optional
+    :param col_wrap: Maximum number of subplot columns, defaults to 1.
+    :type col_wrap: int, optional
+    :param peak_labels: Peak-labels to include, defaults to None.
+    :type peak_labels: list, optional
+    :param legend: Whether to display legend, defaults to True.
+    :type legend: bool, optional
+    :param verbose: If True, prints additional details, defaults to False.
+    :type verbose: bool, optional
+    :param legend_orientation: Legend orientation, defaults to 'v'.
+    :type legend_orientation: str, optional
+    :param call_show: If True, displays the plot immediately, defaults to False.
+    :type call_show: bool, optional
+    :param palette: Color palette to use, defaults to 'Plasma'.
+    :type palette: str, optional
+
+    :return: Plotly Figure object or None if call_show is True.
+    :rtype: plotly.graph_objs._figure.Figure or None
     """
     mint_results = mint_results.copy()
 
+    # Merge with metadata if provided
+    if mint_metadata is not None:
+        mint_results = pd.merge(mint_results, mint_metadata, left_on='ms_file_label', right_index=True)
 
+    # Filter by filenames
     if fns is not None:
         fns = [fn_to_label(fn) for fn in fns]
         mint_results = mint_results[mint_results.ms_file_label.isin(fns)]
+    else:
+        fns = mint_results.ms_file_label.unique()
+    
+    # Filter by peak_labels
+    if peak_labels is not None:
+        if isinstance(peak_labels, str):
+            peak_labels = [peak_labels]
+        mint_results = mint_results[mint_results.peak_label.isin(peak_labels)]
+    else:
+        peak_labels = mint_results.results.peak_label.unique()
+        
+    # Handle colors based on metadata or fall back to default behavior
+    colors = None
+    if color:
+        unique_hues = mint_results[color].unique()
+
+        colors = get_palette_colors(palette, len(unique_hues)) 
+
+        color_mapping = dict(zip(unique_hues, colors))
+                        
+        if color == 'ms_file_label':
+            hue_column = [color_mapping[fn] for fn in fns]
+        else:
+            # Existing logic remains the same for the else part
+            hue_column = mint_results.drop_duplicates('ms_file_label').set_index('ms_file_label')[color].map(color_mapping).reindex(fns).tolist()
 
-    mint_results.ms_file = [P(fn).name for fn in mint_results.ms_file]
-
-    logging.warning("TEST")
+    else:
+        hue_column = colors
 
+    # Rest of the plotting process
     res = mint_results[mint_results.peak_max > 0]
-
-    fns = res.ms_file_label.unique()
     labels = mint_results.peak_label.unique()
-
     res = res.set_index(["peak_label", "ms_file_label"]).sort_index()
 
-    if isinstance(peak_labels, str):
-        peak_labels = [peak_labels]
-
-    # Calculate neccessary number of rows
+    # Calculate necessary number of rows
     n_rows = max(1, len(labels) // col_wrap)
     if n_rows * col_wrap < len(labels):
         n_rows += 1
 
-    if verbose:
-        print(n_rows, col_wrap)
-        print("ms_files:", fns)
-        print("peak_labels:", peak_labels)
-        print("Data:", res)
-
     fig = make_subplots(
         rows=max(1, n_rows), cols=max(1, col_wrap), subplot_titles=peak_labels
     )
-    if len(fns) < 13:
-        colors = cl.scales["12"]["qual"]["Paired"]
-    else:
-        colors = cl.interp(cl.scales["12"]["qual"]["Paired"], len(fns))
 
-    # Create sub-plots
     for label_i, label in enumerate(peak_labels):
         for file_i, fn in enumerate(fns):
             try:
@@ -282,9 +323,9 @@ def plotly_peak_shapes(
             except KeyError as e:
                 logging.warning(e)
                 continue
+
             if not isinstance(x, Iterable):
                 continue
-
             if isinstance(x, str):
                 x = x.split(",")
                 y = y.split(",")
@@ -297,6 +338,8 @@ def plotly_peak_shapes(
             else:
                 mode = "lines"
 
+            trace_color = trace_color = hue_column[file_i]
+
             fig.add_trace(
                 go.Scatter(
                     x=x,
@@ -305,7 +348,7 @@ def plotly_peak_shapes(
                     mode=mode,
                     legendgroup=file_i,
                     showlegend=(label_i == 0),
-                    marker_color=colors[file_i],
+                    marker_color=trace_color,
                     text=fn,
                 ),
                 row=ndx_r,
@@ -315,10 +358,10 @@ def plotly_peak_shapes(
             fig.update_xaxes(title_text="Scan time [s]", row=ndx_r, col=ndx_c)
             fig.update_yaxes(title_text="Intensity", row=ndx_r, col=ndx_c)
 
-    # Layout
+    # Layout updates
     if legend:
         fig.update_layout(legend_orientation=legend_orientation)
-
+        
     fig.update_layout(showlegend=legend)
     fig.update_layout(height=400 * n_rows, title_text="Peak Shapes")
 
@@ -326,3 +369,17 @@ def plotly_peak_shapes(
         fig.show(config={"displaylogo": False})
     else:
         return fig
+
+
+def get_palette_colors(palette_name, num_colors):
+    # Categories in the colorlover package
+    categories = ["qual", "seq", "div"]
+
+    num_colors = max(num_colors, 3)
+    # Check in which category our palette resides
+    for category in categories:
+        if palette_name in cl.scales[f"{num_colors}"][category]:
+            return cl.scales[f"{num_colors}"][category][palette_name]
+
+    # If palette not found in any category, return a default one or raise an error
+    return cl.scales[f"{num_colors}"]["qual"]["Paired"]

{ms-mint-0.3.1 → ms-mint-0.3.2}/ms_mint/standards.py

@@ -58,4 +58,18 @@ DEPRECATED_LABELS = {
     "ms_file_size": "ms_file_size_MB",
 }
 
+MINT_METADATA_COLUMNS = [
+    'ms_file_label',
+    'label', 
+    'group',
+    'batch',
+    'sample_type',
+    'run_order', 
+    'plate',
+    'plate_row', 
+    'plate_col',
+    'lc_column',
+    'polarity'
+]
+
 M_PROTON = 1.00782503223

{ms-mint-0.3.1 → ms-mint-0.3.2}/ms_mint/tools.py

@@ -8,7 +8,7 @@ from molmass import Formula, FormulaError
 from sklearn.preprocessing import MinMaxScaler, StandardScaler, RobustScaler
 from scipy.signal import find_peaks, peak_widths
 
-from .standards import M_PROTON, TARGETS_COLUMNS
+from .standards import M_PROTON, TARGETS_COLUMNS, MINT_METADATA_COLUMNS
 from .filelock import FileLock
 from .matplotlib_tools import plot_peaks
 
@@ -230,18 +230,9 @@ def mz_mean_width_to_min_max(mz_mean, mz_width):
     mz_max = mz_mean + delta_mass
     return mz_min, mz_max
 
+
 def init_metadata():
-    cols = [
-        'ms_file_label',
-        'ms_file',
-        'label', 
-        'group', 
-        'type',
-        'run_order', 
-        'plate', 
-        'plate_row', 
-        'plate_col'
-    ]
+    cols = MINT_METADATA_COLUMNS
     return pd.DataFrame(columns=cols).set_index('ms_file_label')
 
 

{ms-mint-0.3.1 → ms-mint-0.3.2/ms_mint.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ms-mint
-Version: 0.3.1
+Version: 0.3.2
 Summary: Metabolomics Integrator (Mint)
 Home-page: https://github.com/LewisResearchGroup/ms-mint
 Author: Soren Wacker
@@ -15,6 +15,8 @@ License-File: LICENSE
 [![Python package](https://github.com/LewisResearchGroup/ms-mint/actions/workflows/pythonpackage.yml/badge.svg)](https://github.com/LewisResearchGroup/ms-mint/actions/workflows/pythonpackage.yml)
 ![](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)
+![PyPI](https://img.shields.io/pypi/v/ms-mint?label=pypi%20package)
+![PyPI - Downloads](https://img.shields.io/pypi/dm/ms-mint)
 
 # Wecome to ms-mint
 
@@ -136,7 +138,7 @@ 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.
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-before-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/peak-shapes-before-opt.png)
 
 Now, we can run the peak optimization with:
 
@@ -153,7 +155,7 @@ 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.
     
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/optimize-rt_min_max.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/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.
 
@@ -162,7 +164,7 @@ Then we apply the changes and plot the new peak shapes:
     mint.run()
     mint.plot.peak_shapes(col_wrap=3)
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-after-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/peak-shapes-after-opt.png)
 
 As you can see, the shapes of Xanthine, Succinate, Citrulline look much better.
 
@@ -172,7 +174,7 @@ The `Mint` class has a few convenient methods to visualize and explore the proce
 
 ## Plot peak shapes
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/peak-shapes-after-opt.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/peak-shapes-after-opt.png)
 
     mint.plot.peak_shapes(col_wrap = 3)
 
@@ -207,7 +209,7 @@ Before clustering the data can be transformed and scaled. By default `log2p1(x)
         cmap=None  # Name of a matplotlib color map                
     )
 
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/hierarchical_clustering.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/hierarchical_clustering.png)
 
 ## Principal Components Analysis
 
@@ -221,7 +223,7 @@ After running the PCA the results can be plotted with:
     
     mint.pca.plot.pairplot(n_components=5, interactive=False)
     
-![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/pca-pairplot.png)
+![](https://raw.githubusercontent.com/LewisResearchGroup/ms-mint/develop/notebooks/img/pca-pairplot.png)
 
 ## FAQ
 ### What is a target list