Merge pull request #36 from llegregam/Dev

Dev
llegregam · Apr 3, 2023 · acd7052 · acd7052
2 parents 82198ef + c1f3490
commit acd7052
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Showing 2 changed files with 27 additions and 2 deletions.
diff --git a/ms_reader/__init__.py b/ms_reader/__init__.py
@@ -1 +1 @@
-__version__ = "1.4.0"
+__version__ = "1.4.1"
diff --git a/ms_reader/extract.py b/ms_reader/extract.py
@@ -1069,6 +1069,16 @@ def _build_stat_output(self, pca):
                 c13_areas.insert(1, "type", "C13 area")
                 to_out.append(c13_areas)
 
+        if isinstance(self.norm_c12_areas, pd.DataFrame):
+            if pca:
+                norm_c12_areas = self._replace(self.norm_c12_areas, ["NA", np.inf, "", "ND"], 0, "dataframe")
+            else:
+                norm_c12_areas = self._replace(self.norm_c12_areas, [0, np.inf, "", "ND"], "NA", "dataframe")
+            norm_c12_areas = norm_c12_areas.reset_index()
+            norm_c12_areas = norm_c12_areas.rename({"Compound": "features"}, axis=1)
+            norm_c12_areas.insert(1, "type", "Normalised C12 area")
+            to_out.append(norm_c12_areas)
+
         if isinstance(self.ratios, pd.DataFrame):
             ratios = self.ratios.reset_index()
             if pca:
@@ -1079,6 +1089,16 @@ def _build_stat_output(self, pca):
             ratios.insert(1, "type", "C12/C13 ratios")
             to_out.append(ratios)
 
+        if isinstance(self.normalised_ratios, pd.DataFrame):
+            norm_ratios = self.normalised_ratios.reset_index()
+            if pca:
+                norm_ratios = self._replace(norm_ratios, ["NA", np.inf, np.nan, "", "ND"], 0, "dataframe")
+            else:
+                norm_ratios = self._replace(norm_ratios, [np.inf, np.nan, "", "ND"], "NA", "dataframe")
+            norm_ratios = norm_ratios.rename({"Compound": "features"}, axis=1)
+            norm_ratios.insert(1, "type", "Normalised C12/C13 ratios")
+            to_out.append(norm_ratios)
+
         if not pca:
             if isinstance(self.concentration_table, pd.DataFrame) or isinstance(
                     self.loq_table, pd.DataFrame):
@@ -1094,7 +1114,12 @@ def _build_stat_output(self, pca):
                 concentrations = concentrations.reset_index()
                 concentrations = concentrations.rename({"Compound": "features"},
                                                        axis=1)
-                concentrations.insert(1, "type", "concentration")
+                if isinstance(self.quantities, pd.DataFrame) and not isinstance(self.normalised_quantities, pd.DataFrame):
+                    concentrations.insert(1, "type", "Quantity")
+                elif isinstance(self.normalised_quantities, pd.DataFrame):
+                    concentrations.insert(1, "type", "Normalised quantity")
+                elif isinstance(self.concentration_table, pd.DataFrame):
+                    concentrations.insert(1, "type", "Concentration")
                 to_out.append(concentrations)
 
         # if isinstance(self.quantities)