Merge pull request #99 from Roestlab/patch/ui_rename_results_peak_bou…

…ndaries

[CHANGE] ui option name for feature file boundaries

massdash/server/ExtractedIonChromatogramAnalysisServer.py

@@ -127,10 +127,10 @@ def main(self):
             st.write(f"Loading XIC data... Elapsed time: {elapsed_time()}") 
 
             # Perform peak picking based on user settings
-            if peak_picking_settings.do_peak_picking == 'OSW-PyProphet':
+            if peak_picking_settings.do_peak_picking == 'Feature File Boundaries':
                 with time_block() as elapsed_time:
                     tr_group_feature_data = self.xic_data.loadTransitionGroupFeatures(transition_list_ui.transition_settings.selected_peptide, transition_list_ui.transition_settings.selected_charge)
-                st.write(f"Loading OSW-PyProphet Peak Boundaries... Elapsed time: {elapsed_time()}")
+                st.write(f"Loading Feature File Peak Boundaries... Elapsed time: {elapsed_time()}")
             elif peak_picking_settings.do_peak_picking == 'pyPeakPickerMRM':
                 with time_block() as elapsed_time:
                     # Peak picking using pyMRMTransitionGroupPicker

massdash/server/OneDimensionPlotterServer.py

@@ -7,6 +7,8 @@
 from os.path import basename
 import streamlit as st
 
+# Loaders
+from ..loaders.MzMLDataLoader import MzMLDataLoader
 # Plotting
 from ..plotting.GenericPlotter import PlotConfig
 from ..plotting.InteractivePlotter import InteractivePlotter
@@ -45,10 +47,12 @@ class OneDimensionPlotterServer:
 
     def __init__(self, 
                  feature_map_dict: Dict[str, FeatureMap], 
+                 mzml_loader_dict: Dict[str, MzMLDataLoader], 
                  transition_list_ui: TransitionListUISettings, chrom_plot_settings: ChromatogramPlotUISettings, 
                  peak_picking_settings: PeakPickingUISettings, spectral_library_path: str=None,
                  verbose: bool=False):
         self.feature_map_dict = feature_map_dict 
+        self.mzml_loader_dict = mzml_loader_dict
         self.transition_list_ui = transition_list_ui
         self.chrom_plot_settings = chrom_plot_settings
         self.peak_picking_settings = peak_picking_settings
@@ -75,9 +79,9 @@ def generate_chromatogram_plots(self):
                 tr_group = feature_map.to_chromatograms()
                 # Perform peak picking if enabled
                 peak_picker = PeakPickingServer(self.peak_picking_settings, self.chrom_plot_settings)
-                tr_group_feature_data = peak_picker.perform_peak_picking(tr_group_data={'tmp':tr_group}, transition_list_ui=self.transition_list_ui, spec_lib=self.spectral_library_path)
+                tr_group_feature_data = peak_picker.perform_peak_picking(tr_group_data={file:tr_group}, mzml_loader_dict=self.mzml_loader_dict, transition_list_ui=self.transition_list_ui, spec_lib=self.spectral_library_path)
                 plot_settings_dict = self._get_plot_settings('Retention Time (s)', 'Intensity', file, 'chromatogram')
-                plot_obj = self._generate_plot(tr_group, plot_settings_dict, tr_group_feature_data['tmp'])
+                plot_obj = self._generate_plot(tr_group, plot_settings_dict, tr_group_feature_data[file])
                 run_plots_list.append(plot_obj)
 
             # Generate Mobilogram Plot

massdash/server/PeakPickingServer.py

@@ -33,9 +33,9 @@ def __init__(self, peak_picking_settings: PeakPickingUISettings, chrom_plot_sett
         self.peak_picking_settings = peak_picking_settings
         self.chrom_plot_settings = chrom_plot_settings
 
-    def perform_osw_pyprophet_peak_picking(self, xic_data: SqMassLoader, transition_list_ui: Literal['ExtractedIonChromatogramAnalysisUI', 'RawTargetedExtractionAnalysisUI']):
+    def perform_feature_file_peak_picking(self, tr_group_data, mzml_loader_dict, transition_list_ui: Literal['ExtractedIonChromatogramAnalysisUI', 'RawTargetedExtractionAnalysisUI']):
         """
-        Performs peak picking using OSW-PyProphet algorithm.
+        Get peak boundaries from Feature File Boundaries.
 
         Args:
             xic_data (object): The XIC data.
@@ -44,12 +44,13 @@ def perform_osw_pyprophet_peak_picking(self, xic_data: SqMassLoader, transition_
         Returns:
             dict: The transition group feature data.
         """
+
+        tr_group_feature_data = {}
         with time_block() as elapsed_time:
-            tr_group_feature_data = xic_data.loadTransitionGroupFeature(
-                transition_list_ui.transition_settings.selected_peptide,
-                transition_list_ui.transition_settings.selected_charge
-            )
-        st.write(f"Loading OSW-PyProphet Peak Boundaries... Elapsed time: {elapsed_time()}")
+            for file in tr_group_data.keys():
+                tr_group_feature_data[file] = mzml_loader_dict.loadTransitionGroupFeatures(transition_list_ui.transition_settings.selected_peptide,
+                transition_list_ui.transition_settings.selected_charge)[file]
+        st.write(f"Loading Feature File Peak Boundaries... Elapsed time: {elapsed_time()}")
         return tr_group_feature_data
 
     def perform_pypeakpicker_mrm_peak_picking(self, tr_group_data: TransitionGroup):
@@ -133,7 +134,7 @@ def perform_conformer_peak_picking(self, spec_lib_path: str, tr_group_data: Tran
         st.write(f"Performing Conformer Peak Picking... Elapsed time: {elapsed_time()}")
         return tr_group_feature_data
 
-    def perform_peak_picking(self, tr_group_data: TransitionGroup=None, xic_data: SqMassLoader=None, transition_list_ui: Literal['ExtractedIonChromatogramAnalysisUI', 'RawTargetedExtractionAnalysisUI']=None, spec_lib: str=None):
+    def perform_peak_picking(self, tr_group_data: TransitionGroup=None, xic_data: SqMassLoader=None, mzml_loader_dict=None, transition_list_ui: Literal['ExtractedIonChromatogramAnalysisUI', 'RawTargetedExtractionAnalysisUI']=None, spec_lib: str=None):
         """
         Performs peak picking based on the selected method.
 
@@ -149,8 +150,8 @@ def perform_peak_picking(self, tr_group_data: TransitionGroup=None, xic_data: Sq
         tr_group_feature_data = {}
 
         # Perform peak picking based on the selected method
-        if self.peak_picking_settings.do_peak_picking == 'OSW-PyProphet':
-            tr_group_feature_data = self.perform_osw_pyprophet_peak_picking(xic_data, transition_list_ui)
+        if self.peak_picking_settings.do_peak_picking == 'Feature File Boundaries':
+            tr_group_feature_data = self.perform_feature_file_peak_picking(tr_group_data, mzml_loader_dict, transition_list_ui)
         elif self.peak_picking_settings.do_peak_picking == 'pyPeakPickerMRM':
             tr_group_feature_data = self.perform_pypeakpicker_mrm_peak_picking(tr_group_data)
         elif self.peak_picking_settings.do_peak_picking == 'MRMTransitionGroupPicker':

massdash/server/RawTargetedExtractionAnalysisServer.py

@@ -202,7 +202,7 @@ def main(self):
                 # Initialize plot object dictionary
                 plot_obj_dict = {}
                 if chrom_plot_settings.display_plot_dimension_type == "1D":
-                    plot_obj_dict = OneDimensionPlotterServer(featureMaps, transition_list_ui, chrom_plot_settings, peak_picking_settings, self.massdash_gui.file_input_settings.transition_list_file_path, self.massdash_gui.verbose).generate_chromatogram_plots().plot_obj_dict
+                    plot_obj_dict = OneDimensionPlotterServer(featureMaps, self.mzml_loader, transition_list_ui, chrom_plot_settings, peak_picking_settings, self.massdash_gui.file_input_settings.transition_list_file_path, self.massdash_gui.verbose).generate_chromatogram_plots().plot_obj_dict
                 elif chrom_plot_settings.display_plot_dimension_type == "2D":
                     plot_obj_dict = TwoDimensionPlotterServer(featureMaps, transition_list_ui, chrom_plot_settings).generate_two_dimensional_plots().plot_obj_dict
                 elif chrom_plot_settings.display_plot_dimension_type == "3D":

massdash/ui/PeakPickingUISettings.py

@@ -45,7 +45,7 @@ def create_ui(self, plot_settings: ChromatogramPlotUISettings):
         st.sidebar.title("Peak Picking")
 
         ## Perform Peak Picking
-        self.do_peak_picking = st.sidebar.selectbox("Peak Picking", ['none', 'OSW-PyProphet', 'pyPeakPickerMRM', 'MRMTransitionGroupPicker', 'Conformer'], help="Peak picking method to use.")
+        self.do_peak_picking = st.sidebar.selectbox("Peak Picking", ['none', 'Feature File Boundaries', 'pyPeakPickerMRM', 'MRMTransitionGroupPicker', 'Conformer'], help="Peak picking method to use.")
 
         if self.do_peak_picking != 'none':
             ## Perform peak picking on displayed chromatogram, or adjust smoothing separately for peak picking?
@@ -54,7 +54,7 @@ def create_ui(self, plot_settings: ChromatogramPlotUISettings):
         if self.do_peak_picking == "pyPeakPickerMRM":
             self.peak_picker_algo_settings = pyPeakPickerMRMUISettings(self)
             self.peak_picker_algo_settings.create_ui(plot_settings)
-        elif self.do_peak_picking == "OSW-PyProphet":
+        elif self.do_peak_picking == "Feature File Boundaries":
             pass
         elif self.do_peak_picking == "MRMTransitionGroupPicker":
             self.peak_picker_algo_settings = MRMTransitionGroupPickerUISettings(self)