ms-mint 0.3.2__tar.gz → 0.3.3__tar.gz

{ms-mint-0.3.2/ms_mint.egg-info → ms-mint-0.3.3}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ms-mint
-Version: 0.3.2
+Version: 0.3.3
 Summary: Metabolomics Integrator (Mint)
 Home-page: https://github.com/LewisResearchGroup/ms-mint
 Author: Soren Wacker

{ms-mint-0.3.2 → ms-mint-0.3.3}/ms_mint/MintPlotter.py

@@ -235,7 +235,7 @@ 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, filters=None, **kwargs):
+    def chromatogram(self, fns=None, peak_labels=None, interactive=False, filters=None, ax=None, **kwargs):
         """Plot the chromatogram extracted from one or more files.
 
         :param fns: File names to extract chromatogram from.
@@ -283,18 +283,28 @@ class MintPlotter:
                 linewidth=0,
             )
             params.update(kwargs)
-            g = sns.relplot(data=data, **params)
-
-            for peak_label, ax in zip(peak_labels, g.axes.flatten()):
-                _, _, rt_min, rt_max = self.mint.get_target_params(
-                    peak_label
-                )
-                if rt_min is not None and rt_max is not None:
-                    ax.axvspan(rt_min, rt_max, color="lightgreen", alpha=0.5, zorder=-1)
-                ax.ticklabel_format(
-                    style="sci", axis="y", useOffset=False, scilimits=(0, 0)
-                )
-            g.set_titles(template="{col_name}")
+            
+            if ax is None:
+                g = sns.relplot(data=data, **params)
+                         
+                for peak_label, ax in zip(peak_labels, g.axes.flatten()):
+                    _, _, rt_min, rt_max = self.mint.get_target_params(
+                        peak_label
+                    )
+                    if rt_min is not None and rt_max is not None:
+                        ax.axvspan(rt_min, rt_max, color="lightgreen", alpha=0.5, zorder=-1)
+                    ax.ticklabel_format(
+                        style="sci", axis="y", useOffset=False, scilimits=(0, 0)
+                    )
+                g.set_titles(template="{col_name}")
+            
+            else:
+                g = sns.lineplot(data=data, 
+                                 x="scan_time",
+                                 y="intensity",
+                                 hue='ms_file_label',
+                                 ax=ax,
+                                 **kwargs)
             return g
 
         else:

{ms-mint-0.3.2 → ms-mint-0.3.3}/ms_mint/_version.py

@@ -8,11 +8,11 @@ import json
 
 version_json = '''
 {
- "date": "2023-08-18T12:58:02-0600",
+ "date": "2023-08-22T11:34:29-0600",
  "dirty": false,
  "error": null,
- "full-revisionid": "2563246318a0e00988500da34daed80721f81b98",
- "version": "v0.3.2"
+ "full-revisionid": "64a5dc5327b4ff4c4c58498b79d6c63b534f52aa",
+ "version": "v0.3.3"
 }
 '''  # END VERSION_JSON
 

{ms-mint-0.3.2 → ms-mint-0.3.3}/ms_mint/matplotlib_tools.py

@@ -212,29 +212,35 @@ def plot_peak_shapes(
                     "Scan time [s]": peak_rt,
                     "Intensity": peak_int,
                     "ms_file_label": ms_file_label,
-                    "peak_label": peak_label + f"\nm/z={mz:.3f}",
+                    "peak_label": peak_label,
                     "Expected Scan time [s]": rt,
                 }
             )
             dfs.append(df)
-
-    df = pd.concat(dfs).reset_index(drop=True)
+    
+    
+    df = pd.concat(dfs, ignore_index=True).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)
+        df = pd.merge(df, mint_metadata, left_on='ms_file_label', right_index=True, how='left')
 
+    _facet_kws = dict(sharex=sharex, sharey=sharey)
+    if 'facet_kws' in kwargs.keys():
+        _facet_kws.update(kwargs.pop('facet_kws'))
+        
     g = sns.relplot(
         data=df,
         x="Scan time [s]",
         y="Intensity",
         hue=hue,
         col="peak_label",
+        col_order=peak_labels,
         kind=kind,
         col_wrap=col_wrap,
         height=height,
         aspect=aspect,
-        facet_kws=dict(sharex=sharex, sharey=sharey),
+        facet_kws=_facet_kws,
         legend=legend,
         **kwargs,
     )

{ms-mint-0.3.2 → ms-mint-0.3.3}/ms_mint/processing.py

@@ -231,8 +231,8 @@ def extract_ms1_properties(array, mz_mean):
     peak_max = intensities.max()
     peak_min = intensities.min()
     peak_median = np.median(intensities)
-
-    peak_rt_of_max = times[masses.argmax()]
+    
+    peak_rt_of_max = times[intensities.argmax()]
 
     peak_delta_int = np.abs(intensities[0] - intensities[-1])
 

{ms-mint-0.3.2 → ms-mint-0.3.3/ms_mint.egg-info}/PKG-INFO

@@ -1,6 +1,6 @@
 Metadata-Version: 2.1
 Name: ms-mint
-Version: 0.3.2
+Version: 0.3.3
 Summary: Metabolomics Integrator (Mint)
 Home-page: https://github.com/LewisResearchGroup/ms-mint
 Author: Soren Wacker