#53 ADD docs viz.xic_plot.py

alpharaw/viz/xic_plot.py

@@ -50,33 +50,36 @@ def plot(
         create_new_fig=True,
         plot_rows=1,
         ith_plot_row=0,
-    ):
+    )->go.Figure:
         """
-        _summary_
+        Main entry of `XIC_Plot`.
 
         Parameters
         ----------
         spectrum_df : pd.DataFrame
-            _description_
+            The spectrum dataframe in alpharaw format
         peak_df : pd.DataFrame
-            _description_
+            The peak dataframe in alpharaw format
         query_df : pd.DataFrame
-            _description_
+            The query dataframe generated by:
+            :func:`alpharaw.viz.df_utils.make_query_df_for_peptide`, or
+            :func:`alpharaw.viz.df_utils.make_query_df`
         title : str, optional
-            _description_, by default ""
+            Plot title, by default ""
         add_peak_area : bool, optional
-            _description_, by default False
+            If add peak area in the hover text, by default False
         create_new_fig : bool, optional
-            _description_, by default True
+            If create a new figure, otherwise plot in `self.fig`, by default True
         plot_rows : int, optional
-            _description_, by default 1
+            If create_new_fig, how many rows (subplots) to create, by default 1
         ith_plot_row : int, optional
-            _description_, by default 0
+            If not create_new_fig, this parameter refers to the row number 
+            in `self.fig`, by default 0
 
         Returns
         -------
-        _type_
-            _description_
+        go.Figure
+            XIC plot figure
         """
         if "rt_sec" in query_df.columns:
             rt_sec = query_df.rt_sec.values[0]
@@ -208,7 +211,47 @@ def plot_query_masses(
         create_new_fig=True,
         plot_rows=1,
         ith_plot_row=0,
-    ):
+    )->go.Figure:
+        """
+        The other entry of `XIC_Plot`
+
+        Parameters
+        ----------
+        spectrum_df : pd.DataFrame
+            The spectrum dataframe in alpharaw format
+        peak_df : pd.DataFrame
+            The peak dataframe in alpharaw format
+        query_masses : np.ndarray
+            The query m/z values to extract XIC profiles
+        query_ion_names : typing.List[str]
+            The query ion names
+        query_rt_sec : float
+            RT in seconds
+        precursor_left_mz : float
+            Left m/z of precursor window for given queries to extract XIC
+        precursor_right_mz : float
+            Right m/z of precursor window for given queries to extract XIC
+        marker_colors : list, optional
+            Colors of each XIC profile, by default None
+        other_plot_infos : typing.List[str], optional
+            Other plot information for hover text, by default None
+        query_intensities : np.ndarray, optional
+            Query intensities for mirror plot, by default None
+        title : str, optional
+            Plot title, by default ""
+        create_new_fig : bool, optional
+            If create a new figure, otherwise plot in `self.fig`, by default True
+        plot_rows : int, optional
+            If create_new_fig, how many rows (subplots) to create, by default 1
+        ith_plot_row : int, optional
+            If not create_new_fig, this parameter refers to the row number 
+            in `self.fig`, by default 0
+
+        Returns
+        -------
+        go.Figure
+            XIC plot figure
+        """
         if create_new_fig:
             self._init_plot(rows=plot_rows)
         mass_tols = (
@@ -422,7 +465,7 @@ def get_peak_area(
     precursor_right_mz: float = -1.0,
 ) -> np.ndarray:
     """
-    Get peak area values for each of the `query_masses`
+    Get peak area values for each of query in `query_masses`
 
     Parameters
     ----------
@@ -435,18 +478,18 @@ def get_peak_area(
     mass_tols : np.ndarray
         The query m/z tolerance in Da
     query_start_rt_sec : float
-        _description_
+        Start RT in seconds
     query_stop_rt_sec : float
-        _description_
-    precursor_left_mz : float, optional
-        _description_, by default -1.0
-    precursor_right_mz : float, optional
-        _description_, by default -1.0
+        Stop RT in seconds
+    precursor_left_mz : float
+        Left m/z of precursor window for given queries to extract XIC
+    precursor_right_mz : float
+        Right m/z of precursor window for given queries to extract XIC
 
     Returns
     -------
     np.ndarray
-        _description_
+        peak area values for each of query
     """
     spec_idxes = get_spec_idxes_from_df(
         spectrum_df,