Merge pull request #62 from MannLabs/53-docs-viz-ii

53 docs viz ii

alpharaw/viz/xic_plot.py

@@ -17,8 +17,15 @@
 
 
 class XIC_Plot:
-    # hovermode = "x" | "y" | "closest" | False | "x unified" | "y unified"
+    """
+    Only apply for 3D-MS, i.e. without mobility
+    """
+
     hovermode = "closest"
+    """
+    hovermode = "x", "y", "closest", False, "x unified", "y unified"
+    """
+
     plot_height = 550
     colorscale_qualitative = "Alphabet"
     colorscale_sequential = "Viridis"
@@ -33,10 +40,6 @@ class XIC_Plot:
     # list of XIC_Trace objects
     traces: list = []
 
-    """
-    Only apply for 3D-MS, i.e. without mobility
-    """
-
     def plot(
         self,
         spectrum_df: pd.DataFrame,
@@ -47,7 +50,37 @@ def plot(
         create_new_fig=True,
         plot_rows=1,
         ith_plot_row=0,
-    ):
+    ) -> go.Figure:
+        """
+        Main 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_df : pd.DataFrame
+            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
+            Plot title, by default ""
+        add_peak_area : bool, optional
+            If add peak area in the hover text, by default False
+        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 "rt_sec" in query_df.columns:
             rt_sec = query_df.rt_sec.values[0]
         else:
@@ -178,7 +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 = (
@@ -391,6 +464,33 @@ def get_peak_area(
     precursor_left_mz: float = -1.0,
     precursor_right_mz: float = -1.0,
 ) -> np.ndarray:
+    """
+    Get peak area values for each of query in `query_masses`
+
+    Parameters
+    ----------
+    spectrum_df : pd.DataFrame
+        The spectrum dataframe
+    peak_df : pd.DataFrame
+        The peak dataframe
+    query_masses : np.ndarray
+        The query m/z values
+    mass_tols : np.ndarray
+        The query m/z tolerance in Da
+    query_start_rt_sec : float
+        Start RT in seconds
+    query_stop_rt_sec : float
+        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
+        peak area values for each of query
+    """
     spec_idxes = get_spec_idxes_from_df(
         spectrum_df,
         query_start_rt_sec=query_start_rt_sec,