Merge pull request #17 from MannLabs/development

Development

HISTORY.md

@@ -1,14 +1,17 @@
 ## Changelog
 
+### 1.1.2
+* FIX: Correct the bug with MS2 intensity prediction using deep learning.
+* FIX: Correct the hover information/color for the MS2 spectrum for the predicted ion intensities.
+* FIX: Fix the behaviour of the "Previous/Next frame" & "Overlay frames" buttons for DDA data analyzed by MaxQuant.
+
 ### 1.1.0
 * FEAT: Integrate the AlphaPeptDeep package into AlphaViz to predict the peptide properties, such as the MS2 intensity prediction for DDA data and retention time/ion mobility prediction for DIA data.
 * FEAT: Update the Quality Control tab to make it lighter than the previous version. Variables for plots (m/z, im, rt, length, etc. distributions) can now be selected.
 * FEAT: Reorganize the Settings panel and add more customization options.
 * DOCS: Extend Jupyter notebooks for manual visual inspection of timsTOF DDA and DIA data analyzed by MaxQuant and DIA-NN, respectively.
 
-
 ### 1.0.5
-
 * FEAT: Enable the possibility to read DIA data analysed by the DIA-NN software analysis tool.
 * FEAT: Extend the "Quality Control" tab with a summary statistics table and additional plots.
 * FEAT: Add a "Targeted Mode" tab to work with raw data only.
@@ -17,6 +20,5 @@
 * FIX: Correct the error when reading the MQ output files (missing columns).
 
 ### 0.0.1
-
 * FEAT: Initial creation of alphaviz.
 * FEAT: Read DDA Bruker data processed with MaxQuant software.

alphaviz/__init__.py

@@ -1,7 +1,7 @@
 #!python
 
 __project__ = "alphaviz"
-__version__ = "1.1.1"
+__version__ = "1.1.2"
 __license__ = "Apache"
 __description__ = "A interactive Dashboard to explore mass spectrometry data."
 __author__ = "Eugenia Voytik"

alphaviz/gui.py

@@ -2,7 +2,9 @@
 import logging
 import platform
 import json
+import warnings
 import pandas as pd
+from pandas.core.common import SettingWithCopyWarning
 from io import StringIO
 
 import alphatims.bruker
@@ -21,6 +23,8 @@
 import alphaviz.preprocessing
 import alphaviz.plotting
 
+warnings.simplefilter(action="ignore", category=SettingWithCopyWarning)
+
 
 def get_css_style(
     file_name="dashboard_style.css",
@@ -506,6 +510,7 @@ def load_data(self, *args):
 
                 self.psm_df['nce'] = 30
                 self.psm_df['instrument'] = 'timsTOF'  # trained on more Lumos files therefore should work better than 'timsTOF'
+                self.psm_df['spec_idx'] += 1
 
         self.trigger_dependancy()
         self.upload_progress.active = False
@@ -886,19 +891,22 @@ def __init__(self, data, options):
             button_type='default',
             width=250,
             align='center',
+            disabled=True,
             margin=(25, 0, 0, 10),
         )
         self.export_svg_ms2_button = pn.widgets.Button(
             name='Export as .svg',
             button_type='default',
             align='center',
+            disabled=True,
             width=250,
             margin=(25, 0, 0, 10),
         )
         self.export_svg_elprofiles_button = pn.widgets.Button(
             name='Export as .svg',
             button_type='default',
             align='center',
+            disabled=True,
             width=250,
             margin=(25, 0, 0, 10),
         )
@@ -1443,10 +1451,9 @@ def display_heatmap_spectrum(self, *args):
                 ms2_frame = self.ms2_frame
                 mz = self.peptide['mz']
                 im = self.peptide['im']
-            data_ms1 = self.data.raw_data[ms1_frame].copy()
             try:
                 self.heatmap_ms1_plot = alphaviz.plotting.plot_heatmap(
-                    data_ms1,
+                    self.data.raw_data[ms1_frame],
                     mz=mz,
                     im=im,
                     x_axis_label=self.heatmap_x_axis.value,
@@ -1460,9 +1467,8 @@ def display_heatmap_spectrum(self, *args):
                     height=450,
                     margin=(0, 10, 10, 0),
                 )
-                data_ms2 = self.data.raw_data[ms2_frame].copy()
                 self.heatmap_ms2_plot = alphaviz.plotting.plot_heatmap(
-                    data_ms2,
+                    self.data.raw_data[ms2_frame],
                     x_axis_label=self.heatmap_x_axis.value,
                     y_axis_label=self.heatmap_y_axis.value,
                     title=f'MS2 frame(s) #{ms2_frame}',
@@ -1472,7 +1478,12 @@ def display_heatmap_spectrum(self, *args):
                     height=450,
                     margin=(0, 10, 10, 0),
                 )
-
+                self.layout[10] = pn.Row(
+                    None,
+                    None,
+                    align='center',
+                    sizing_mode='stretch_width'
+                )
                 self.layout[10][0] = pn.Column(
                     pn.pane.HoloViews(
                         self.heatmap_ms1_plot,
@@ -1495,13 +1506,21 @@ def display_heatmap_spectrum(self, *args):
                 )
             except ValueError:
                 print('The x- and y-axis of the heatmaps should be different.')
+            except BaseException as x:
+                print('The heatmaps cannot be displayed.')
             if self.analysis_software == 'diann':
                 if self.x_axis_label_diann.value == 'RT/IM dimension':
                     self.display_elution_profile_plots()
             if self.analysis_software == 'maxquant':
-                self.layout[9][0] = self.previous_frame
-                self.layout[9][1] = self.next_frame
-                self.layout[11] = self.plot_overlapped_frames
+                for each in [self.previous_frame, self.next_frame, self.plot_overlapped_frames]:
+                    if len(self.ms1_ms2_frames.keys()) < 2:
+                        each.disabled = True
+                    else:
+                        each.disabled = False
+                if type(self.layout[9][0]) == pn.pane.markup.Str:
+                    self.layout[9][0] = self.previous_frame
+                    self.layout[9][1] = self.next_frame
+                    self.layout[11] = self.plot_overlapped_frames
                 self.display_mass_spectrum()
 
     def display_mass_spectrum(self, *args):
@@ -1527,7 +1546,6 @@ def display_mass_spectrum(self, *args):
             predicted_df['FragmentMz'] = mz_ions.b_z1.values.tolist() + mz_ions.y_z1.values.tolist()[::-1]
             predicted_df['RelativeIntensity'] = intensities_ions.b_z1.values.tolist() + intensities_ions.y_z1.values.tolist()[::-1]
             predicted_df['ions'] = [f"b{i}" for i in range(1, len(mz_ions.b_z1)+1)] + [f"y{i}" for i in range(1, len(mz_ions.y_z1)+1)]
-
         self.ms_spectra_plot = alphaviz.plotting.plot_complex_ms_plot(
             data_ions,
             title=f'MS2 spectrum for Precursor: {self.ms1_ms2_frames[self.current_frame][1]}',
@@ -1551,15 +1569,15 @@ def display_previous_frame(self, *args):
             self.layout[12].loading = True
         except IndexError:
             pass
-        self.plot_overlapped_frames.value = False
         current_frame_index = list(self.ms1_ms2_frames.keys()).index(self.current_frame)
         if current_frame_index == 0:
             self.current_frame = list(self.ms1_ms2_frames.keys())[-1]
         else:
             self.current_frame = list(self.ms1_ms2_frames.keys())[current_frame_index - 1]
-        if self.x_axis_label_mq.value == 'm/z':
-            self.display_line_spectra_plots()
-        self.display_heatmap_spectrum()
+        if self.plot_overlapped_frames.value == True:
+            self.plot_overlapped_frames.value = False
+        else:
+            self.display_heatmap_spectrum()
 
     def display_next_frame(self, *args):
         try:
@@ -1568,15 +1586,15 @@ def display_next_frame(self, *args):
             self.layout[12].loading = True
         except IndexError:
             pass
-        self.plot_overlapped_frames.value = False
         current_frame_index = list(self.ms1_ms2_frames.keys()).index(self.current_frame)
         if current_frame_index == len(self.ms1_ms2_frames.keys())-1:
             self.current_frame = list(self.ms1_ms2_frames.keys())[0]
         else:
             self.current_frame = list(self.ms1_ms2_frames.keys())[current_frame_index + 1]
-        if self.x_axis_label_mq.value == 'm/z':
-            self.display_line_spectra_plots()
-        self.display_heatmap_spectrum()
+        if self.plot_overlapped_frames.value == True:
+            self.plot_overlapped_frames.value = False
+        else:
+            self.display_heatmap_spectrum()
 
     def display_overlapped_frames(self, *args):
         try:
@@ -1586,6 +1604,8 @@ def display_overlapped_frames(self, *args):
         except IndexError:
             pass
         if self.plot_overlapped_frames.value is True:
+            self.layout[12] = None
+            self.layout[13] = None
             mz = float(self.peptides_table.value.iloc[self.peptides_table.selection[0]]['m/z'])
             im = float(self.peptides_table.value.iloc[self.peptides_table.selection[0]]['1/K0'])
             try:
@@ -1613,6 +1633,12 @@ def display_overlapped_frames(self, *args):
                     height=450,
                     margin=(0, 10, 10, 0),
                 )
+                self.layout[10] = pn.Row(
+                    None,
+                    None,
+                    align='center',
+                    sizing_mode='stretch_width'
+                )
                 self.layout[10][0] = pn.Column(
                     pn.pane.HoloViews(
                         self.heatmap_ms1_plot,
@@ -1633,10 +1659,10 @@ def display_overlapped_frames(self, *args):
                     self.export_svg_ms2_button,
                     align='center',
                 )
-
             except ValueError:
                 print('The x- and y-axis of the heatmaps should be different.')
-            self.layout[12] = None
+            except BaseException as x:
+                print('The heatmaps cannot be displayed.')
         else:
             self.display_heatmap_spectrum()
 
@@ -1981,13 +2007,15 @@ def __init__(self, data, options):
             name='Export as .svg',
             button_type='default',
             align='center',
+            disabled=True,
             width=250,
             margin=(25, 0, 0, 10),
         )
         self.export_svg_prediction_button = pn.widgets.Button(
             name='Export as .svg',
             button_type='default',
             align='center',
+            disabled=True,
             width=250,
             margin=(25, 0, 0, 10),
         )

alphaviz/plotting.py

@@ -318,6 +318,7 @@ def plot_heatmap(
             z_dimension
         )
     )
+
     agg = rasterize(
         dmap,
         width=width,
@@ -565,20 +566,21 @@ def plot_mass_spectra(
                 mode='markers',
                 opacity=0.7,
                 marker=dict(color=b_ion_color, size=1),
-                hovertext=predicted[2],
+                hovertext=predicted[2][predicted_b_ions_ind],
                 hovertemplate='<b>m/z:</b> %{x};<br><b>Intensity:</b> %{y};<br><b>Ion:</b> %{hovertext}.',
                 name='',
                 showlegend=False
             )
         )
+        predicted_y_ions_ind = list(set(predicted[2].index).difference(predicted_b_ions_ind))
         fig.add_trace(
             go.Scatter(
-                x=predicted[0][set(predicted[2].index).difference(predicted_b_ions_ind)],
-                y=predicted[1][set(predicted[2].index).difference(predicted_b_ions_ind)],
+                x=predicted[0][predicted_y_ions_ind],
+                y=predicted[1][predicted_y_ions_ind],
                 mode='markers',
                 opacity=0.7,
-                marker=dict(color=b_ion_color if 'b' in predicted[2] else y_ion_color, size=1),
-                hovertext=predicted[2],
+                marker=dict(color=y_ion_color, size=1),
+                hovertext=predicted[2][predicted_y_ions_ind],
                 hovertemplate='<b>m/z:</b> %{x};<br><b>Intensity:</b> %{y};<br><b>Ion:</b> %{hovertext}.',
                 name='',
                 showlegend=False

misc/bumpversion.cfg

@@ -1,5 +1,5 @@
 [bumpversion]
-current_version = 1.1.1
+current_version = 1.1.2
 commit = True
 tag = False
 parse = (?P<major>\d+)\.(?P<minor>\d+)\.(?P<patch>\d+)(\-(?P<release>[a-z]+)(?P<build>\d+))?

nbs/tutorial_MaxQuant.ipynb

@@ -71,7 +71,7 @@
    "metadata": {},
    "source": [
     "To save the Plotly plots as .svg, you need to add this code with the name of the file inside the show function:\n",
-    "`.show(config=alphaviz.gui.update_config(filename='elution_profile.svg'))`.  \n",
+    "`.show(config=alphaviz.gui.update_config(filename='elution_profile.svg'))` and when the plot is shown, click the \"Download plot\" button on the Plotly tool panel.  \n",
     "\n",
     "You can also specify the height and width of the saved plot. See example for the Chromatogram plot."
    ]
@@ -577,7 +577,7 @@
    "metadata": {},
    "outputs": [],
    "source": [
-    "predlib = model_mgr.predict_all(data_slice, predict_items=['ms2'], frag_types=['b_z1', 'y_z1'])"
+    "predlib = model_mgr.predict_all(data_slice, predict_items=['ms2'], frag_types=['b_z1', 'y_z1'], multiprocessing=False)"
    ]
   },
   {

release/one_click_linux_gui/control

@@ -1,5 +1,5 @@
 Package: alphaviz
-Version: 1.1.1
+Version: 1.1.2
 Architecture: all
 Maintainer: Mann Labs <opensource@alphapept.com>
 Description: alphaviz

release/one_click_linux_gui/create_installer_linux.sh

@@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel
 # Setting up the local package
 cd release/one_click_linux_gui
 # Make sure you include the required extra packages and always use the stable or very-stable options!
-pip install "../../dist/alphaviz-1.1.1-py3-none-any.whl[stable,gui-stable]"
+pip install "../../dist/alphaviz-1.1.2-py3-none-any.whl[stable,gui-stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.2

release/one_click_macos_gui/Info.plist

@@ -9,9 +9,9 @@
 	<key>CFBundleIconFile</key>
 	<string>alpha_logo.icns</string>
 	<key>CFBundleIdentifier</key>
-	<string>alphaviz.1.1.1</string>
+	<string>alphaviz.1.1.2</string>
 	<key>CFBundleShortVersionString</key>
-	<string>1.1.1</string>
+	<string>1.1.2</string>
 	<key>CFBundleInfoDictionaryVersion</key>
 	<string>6.0</string>
 	<key>CFBundleName</key>

release/one_click_macos_gui/create_installer_macos.sh

@@ -20,7 +20,7 @@ python setup.py sdist bdist_wheel
 
 # Setting up the local package
 cd release/one_click_macos_gui
-pip install "../../dist/alphaviz-1.1.1-py3-none-any.whl[stable,gui-stable]"
+pip install "../../dist/alphaviz-1.1.2-py3-none-any.whl[stable,gui-stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.2
@@ -40,5 +40,5 @@ cp ../../LICENSE.txt Resources/LICENSE.txt
 cp ../logos/alpha_logo.png Resources/alpha_logo.png
 chmod 777 scripts/*
 
-pkgbuild --root dist/alphaviz --identifier de.mpg.biochem.alphaviz.app --version 1.1.1 --install-location /Applications/alphaviz.app --scripts scripts alphaviz.pkg
+pkgbuild --root dist/alphaviz --identifier de.mpg.biochem.alphaviz.app --version 1.1.2 --install-location /Applications/alphaviz.app --scripts scripts alphaviz.pkg
 productbuild --distribution distribution.xml --resources Resources --package-path alphaviz.pkg dist/alphaviz_gui_installer_macos.pkg

release/one_click_macos_gui/distribution.xml

@@ -1,6 +1,6 @@
 <?xml version="1.0" encoding="utf-8" standalone="no"?>
 <installer-script minSpecVersion="1.000000">
-    <title>alphaviz 1.1.1</title>
+    <title>alphaviz 1.1.2</title>
     <background mime-type="image/png" file="alpha_logo.png" scaling="proportional"/>
     <welcome file="welcome.html" mime-type="text/html" />
     <conclusion file="conclusion.html" mime-type="text/html" />

release/one_click_windows_gui/alphaviz_innoinstaller.iss

@@ -2,7 +2,7 @@
 ; SEE THE DOCUMENTATION FOR DETAILS ON CREATING INNO SETUP SCRIPT FILES!
 
 #define MyAppName "alphaviz"
-#define MyAppVersion "1.1.1"
+#define MyAppVersion "1.1.2"
 #define MyAppPublisher "Max Planck Institute of Biochemistry and the University of Copenhagen, Mann Labs"
 #define MyAppURL "https://github.com/MannLabs/alphaviz"
 #define MyAppExeName "alphaviz_gui.exe"

release/one_click_windows_gui/create_installer_windows.sh

@@ -17,7 +17,7 @@ python setup.py sdist bdist_wheel
 # Setting up the local package
 cd release/one_click_windows_gui
 # Make sure you include the required extra packages and always use the stable or very-stable options!
-pip install "../../dist/alphaviz-1.1.1-py3-none-any.whl[stable,gui-stable]"
+pip install "../../dist/alphaviz-1.1.2-py3-none-any.whl[stable,gui-stable]"
 
 # Creating the stand-alone pyinstaller folder
 pip install pyinstaller==4.2

requirements/requirements.txt

@@ -1,3 +1,3 @@
 alphatims==0.3.0
-peptdeep==0.0.4
+peptdeep==0.0.5
 alphabase==0.0.5