Visualization options

EngineLayer/FdrAnalysis/PEPValueAnalysisGeneric.cs

@@ -557,6 +557,29 @@ private static double GetCifuentesMobility(PeptideWithSetModifications pwsm)
             return mobility;
         }
 
+        //Mobility based on Charge calculation at a given a pH and ionizable group pKa values. default pH set to 2.4.
+        private static double GetPkaBasedMobility(PeptideWithSetModifications pwsm, double pH = 2.4)
+        {
+            double KCharge = Math.Pow(10, 10.8 - pH) / (1 + Math.Pow(10, 10.8 - pH));
+;           double RCharge = Math.Pow(10, 12.5 - pH) / (1 + Math.Pow(10, 12.5 - pH));
+            double HCharge = Math.Pow(10, 6.5 - pH) / (1 + Math.Pow(10, 6.5 - pH));
+            double NTermCharge = Math.Pow(10, 8.6 - pH) / (1 + Math.Pow(10, 8.6 - pH));
+            double CCharge = Math.Pow(10, pH - 8.5) / (1 + Math.Pow(10, pH - 8.5));
+            double YCharge = Math.Pow(10, pH - 10.1) / (1 + Math.Pow(10, pH - 10.1));
+            double ECharge = Math.Pow(10, pH - 4.1) / (1 + Math.Pow(10, pH - 4.1));
+            double DCharge = Math.Pow(10, pH - 3.9) / (1 + Math.Pow(10, pH - 3.9));
+            double CTermCharge = Math.Pow(10, pH - 3.6) / (1 + Math.Pow(10, pH - 3.6));
+
+            double peptideCharge = NTermCharge + CTermCharge + pwsm.BaseSequence.Count(f => f == 'K') * KCharge + pwsm.BaseSequence.Count(f => f == 'R') * RCharge
+                + pwsm.BaseSequence.Count(f => f == 'H') * HCharge + pwsm.BaseSequence.Count(f => f == 'C') * CCharge +  pwsm.BaseSequence.Count(f => f == 'Y') * YCharge
+                +  pwsm.BaseSequence.Count(f => f == 'E') * ECharge +  pwsm.BaseSequence.Count(f => f == 'D') * DCharge
+                - CountModificationsThatShiftMobility(pwsm.AllModsOneIsNterminus.Values.AsEnumerable());
+
+            double mobility = (Math.Log(1 + 0.35 * peptideCharge)) / Math.Pow(pwsm.MonoisotopicMass, 0.411);
+
+            return mobility;
+        }
+
         private static float GetSSRCalcHydrophobicityZScore(PeptideSpectralMatch psm, PeptideWithSetModifications Peptide, Dictionary<string, Dictionary<int, Tuple<double, double>>> d)
         {
             //Using SSRCalc3 but probably any number of different calculators could be used instead. One could also use the CE mobility.

GUI/Util/BooleanToVisibilityConverter.cs → GUI/Coverters/BooleanToVisibilityConverter.cs

@@ -12,7 +12,7 @@ public class BooleanToVisibilityConverter : BaseValueConverter<BooleanToVisibili
     {
         public override object Convert(object value, Type targetType, object parameter, CultureInfo culture)
         {
-            if (value is Boolean && (bool)value)
+            if (value is bool && (bool)value)
             {
                 return Visibility.Visible;
             }

GUI/Coverters/CheckboxUncheckConverter.cs

@@ -0,0 +1,37 @@
+using System;
+using System.Collections.Generic;
+using System.Globalization;
+using System.Linq;
+using System.Text;
+using System.Threading.Tasks;
+using System.Windows;
+
+namespace MetaMorpheusGUI
+{
+    public class CheckboxUncheckConverter : BaseValueConverter<CheckboxUncheckConverter>
+    {
+        public override object Convert(object value, Type targetType, object parameter, CultureInfo culture)
+        {
+            if ((bool)value)
+            {
+                return false;
+            }
+            else
+            {
+                return (bool)value;
+            }
+        }
+
+        public override object ConvertBack(object value, Type targetType, object parameter, CultureInfo culture)
+        {
+            if (!(bool)value)
+            {
+                return false;
+            }
+            else
+            {
+                return (bool)parameter;
+            }
+        }
+    }
+}

GUI/MetaDraw/MetaDraw.xaml

@@ -242,7 +242,7 @@
                                                 <!-- actual ptm legend -->
                                                 <local:PtmLegendControl x:Name="ChildScanPtmLegendControl"   DataContext="{Binding}" />
                                             </StackPanel>
-                                            
+
                                         </Grid>
                                     </Grid>
                                 </TabItem>
@@ -421,6 +421,7 @@
                 </DockPanel>
             </TabItem>
 
+
             <!--Stats tab-->
             <TabItem Header="Data Visualization" Background="DarkGray">
                 <DockPanel>
@@ -437,8 +438,10 @@
                                 <RowDefinition Height="29"/>
                                 <RowDefinition Height="29"/>
                                 <RowDefinition Height="50*"/>
+                                <RowDefinition Height="40"/>
                                 <RowDefinition Height="40*"/>
                                 <RowDefinition Height="25"/>
+                                <RowDefinition Height="25"/>
                             </Grid.RowDefinitions>
 
                             <!--Select MetaMorpheus output file-->
@@ -467,12 +470,24 @@
                                 </DockPanel>
                             </DockPanel>
 
+                            <DockPanel Grid.Row="3">
+                                <Label Height="25" VerticalAlignment="Top" HorizontalAlignment="Right">Filter Psms by Full Sequence</Label>
+                                <TextBox TextChanged="TextBoxBase_OnTextChanged" DockPanel.Dock="Left" Width="125" Height="30" VerticalAlignment="Top" ToolTip="Shows only PSMs where the Full sequence (including PTMs) contains the value of this text box"/>
+                            </DockPanel>
+
                             <!--List of plot options-->
-                            <GroupBox Header="Plot Type" Name="plotType" Grid.Row="3">
+                            <GroupBox Header="Plot Type" Name="plotType" Grid.Row="4">
                                 <ListView x:Name="plotsListBox" ItemsSource="{Binding}" SelectionChanged ="PlotSelected" MaxHeight="400"/>
                             </GroupBox>
 
-                            <DockPanel Grid.Row="4" Margin="2">
+                            <!--Whether to display y-axis on a log scale-->
+                            <DockPanel Grid.Row="5" Margin="5,5,0,0">
+                                <CheckBox Name="yAxisLogScaleCheckbox" Content="y-axis log scale" IsChecked="False" Checked="YAxisLogScaleCheckbox_OnChecked" Unchecked="YAxisLogScaleCheckbox_OnUnchecked" Margin="0,0,10,0" ToolTip="Displays histogram y-axis on a logarithmic scale when checked"></CheckBox>
+                                <CheckBox Name="stackedBars" Content="Stacked Bars" IsChecked="True" Checked="StackedBars_OnChecked" Unchecked="StackedBars_OnUnchecked" Margin="0,0,10,0" ToolTip="Stacks histogram bars for multiple files when checked"></CheckBox>
+                                <CheckBox Name ="invertFilter" Content="Invert Filter" IsChecked="False" Checked="InvertFilter_OnChecked" Unchecked="InvertFilter_OnUnchecked" ToolTip="Displays PSMs that DO NOT pass the Full Sequence filter"></CheckBox>
+                            </DockPanel>
+
+                            <DockPanel Grid.Row="6" Margin="2">
                                 <Button Content="Export to PDF" Width="100" Click="CreatePlotPdf_Click" />
                             </DockPanel>
                         </Grid>

GUI/MetaDraw/MetaDraw.xaml.cs

@@ -23,6 +23,9 @@
 using System.Windows.Input;
 using System.Windows.Media;
 using System.Windows.Media.Imaging;
+using Easy.Common.Extensions;
+using Org.BouncyCastle.Asn1.Crmf;
+using OxyPlot.Wpf;
 
 namespace MetaMorpheusGUI
 {
@@ -43,6 +46,8 @@ public partial class MetaDraw : Window
         private static List<string> AcceptedResultsFormats = new List<string> { ".psmtsv", ".tsv" };
         private static List<string> AcceptedSpectralLibraryFormats = new List<string> { ".msp" };
         private SettingsViewModel SettingsView;
+        private string searchString = string.Empty;
+        private bool plotInverseBool = false;
 
         public MetaDraw()
         {
@@ -737,13 +742,47 @@ private async void PlotSelected(object sender, SelectionChangedEventArgs e)
             Dictionary<string, ObservableCollection<PsmFromTsv>> psmsBSF = new Dictionary<string, ObservableCollection<PsmFromTsv>>();
             foreach (string fileName in selectSourceFileListBox.SelectedItems)
             {
-                psmsBSF.Add(fileName, MetaDrawLogic.PsmsGroupedByFile[fileName]);
+                //pull out those PSMs for each file that have a full sequence matching the filter
+                var filteredPSMsForPlotsBSF = MetaDrawLogic.PsmsGroupedByFile[fileName]
+                    .Where(p => p.FullSequence.ToUpper().Contains(searchString));
+                if (!filteredPSMsForPlotsBSF.Any()) continue;
+
+                //If the inverse box is checked, take the opposite PSMs
+                if (plotInverseBool)
+                {
+                    filteredPSMsForPlotsBSF = MetaDrawLogic.PsmsGroupedByFile[fileName]
+                        .Where(p => !p.FullSequence.ToUpper().Contains(searchString));
+                }
+
+                //Save PSMs as observable collection
+                var filteredPSMsForPLotsBSFOC = new ObservableCollection<PsmFromTsv>(filteredPSMsForPlotsBSF);
+                psmsBSF.Add(fileName, filteredPSMsForPLotsBSFOC);
                 foreach (PsmFromTsv psm in MetaDrawLogic.PsmsGroupedByFile[fileName])
                 {
                     psms.Add(psm);
                 }
             }
-            PlotModelStat plot = await Task.Run(() => new PlotModelStat(plotName, psms, psmsBSF));
+
+            //Filter all PSMs that pass the filter
+            var filteredPSMsForPlots = psms.Where(p => p.FullSequence.ToUpper().Contains(searchString));
+
+            //check that there are some PSMs
+            if (!filteredPSMsForPlots.Any())
+            {
+                MessageBox.Show("No PSMs pass the filter");
+                return;
+            }
+
+            //If the inverse box is checked, take the opposite PSMs
+            if (plotInverseBool)
+            {
+                filteredPSMsForPlots = psms.Where(p => !p.FullSequence.ToUpper().Contains(searchString.ToUpper()));
+            }
+
+            //Save as observable collection
+            var filteredPSMsForPlotsOC = new ObservableCollection<PsmFromTsv>(filteredPSMsForPlots);
+            //Create the PlotModelStat with the filtered psms
+            PlotModelStat plot = await Task.Run(() => new PlotModelStat(plotName, filteredPSMsForPlotsOC, psmsBSF));
             plotViewStat.DataContext = plot;
             PlotViewStat_SizeChanged(plotViewStat, null);
         }
@@ -1016,7 +1055,7 @@ private void ClearPresentationArea()
         /// <param name="value">true = enabled, false = disable</param>
         private void ToggleButtonsEnabled(bool value)
         {
-            loadFiles.IsEnabled = value;
+            loadFiles.IsEnabled = value; 
             selectSpectraFileButton.IsEnabled = value;
             selectPsmFileButton.IsEnabled = value;
             selectSpecLibraryButton.IsEnabled = value;
@@ -1025,5 +1064,63 @@ private void ToggleButtonsEnabled(bool value)
             resetSpectraFileButton.IsEnabled = value;
             ExportButton.IsEnabled = value;
         }
+
+        private void YAxisLogScaleCheckbox_OnChecked(object sender, RoutedEventArgs e)
+        {
+            if (MetaDrawSettings.stackedBool)
+            {
+                MessageBox.Show("Stacked bars with logarithmic scale not recommended");
+            }
+            MetaDrawSettings.yAxisLogScale = yAxisLogScaleCheckbox.IsChecked.Value;
+            if (MetaDrawLogic != null)
+                PlotSelected(plotsListBox, null);
+        }
+
+        private void YAxisLogScaleCheckbox_OnUnchecked(object sender, RoutedEventArgs e)
+        {
+            MetaDrawSettings.yAxisLogScale = yAxisLogScaleCheckbox.IsChecked.Value;
+            if (MetaDrawLogic != null)
+                PlotSelected(plotsListBox, null);
+        }
+
+        private void StackedBars_OnChecked(object sender, RoutedEventArgs e)
+        {
+            if (MetaDrawSettings.yAxisLogScale)
+            {
+                MessageBox.Show("Stacked bars with logarithmic scale not recommended");
+            }
+            MetaDrawSettings.stackedBool = stackedBars.IsChecked.Value;
+            if (MetaDrawLogic != null)
+                PlotSelected(plotsListBox, null);
+        }
+
+        private void StackedBars_OnUnchecked(object sender, RoutedEventArgs e)
+        {
+            MetaDrawSettings.stackedBool = stackedBars.IsChecked.Value;
+            if (MetaDrawLogic != null)
+                PlotSelected(plotsListBox, null);
+        }
+
+        private void TextBoxBase_OnTextChanged(object sender, TextChangedEventArgs e)
+        {
+            string txt = (sender as TextBox).Text;
+            searchString = txt.ToUpper();
+            if (MetaDrawLogic != null)
+                PlotSelected(plotsListBox, null);
+        }
+
+        private void InvertFilter_OnChecked(object sender, RoutedEventArgs e)
+        {
+            plotInverseBool = invertFilter.IsChecked.Value;
+            if (MetaDrawLogic != null)
+                PlotSelected(plotsListBox, null);
+        }
+
+        private void InvertFilter_OnUnchecked(object sender, RoutedEventArgs e)
+        {
+            plotInverseBool = invertFilter.IsChecked.Value;
+            if (MetaDrawLogic != null)
+                PlotSelected(plotsListBox, null);
+        }
     }
 }

GuiFunctions/MetaDraw/MetaDrawSettings.cs

@@ -93,6 +93,9 @@ public static class MetaDrawSettings
         public static int SequenceAnnotationSegmentPerRow { get; set; } = 3;
         public static int SequenceAnnotaitonResiduesPerSegment { get; set; } = 10;
 
+        public static bool yAxisLogScale { get; set; } = false;
+        public static bool stackedBool { get; set; } = true;
+
         static MetaDrawSettings()
         {
             InitializeDictionaries();
@@ -248,6 +251,8 @@ public static MetaDrawSettingsSnapshot MakeSnapShot()
                 SpectrumDescriptionValues = SpectrumDescription.Values.ToList(),
                 UnannotatedPeakColor = UnannotatedPeakColor.GetColorName(),
                 InternalIonColor = InternalIonColor.GetColorName(),
+                yAxisLogScale = yAxisLogScale,
+                stackedBool = stackedBool,
             };
         }
 
@@ -271,6 +276,8 @@ public static void LoadSettings(MetaDrawSettingsSnapshot settings)
             LocalizationLevelStart = settings.LocalizationLevelStart;
             LocalizationLevelEnd = settings.LocalizationLevelEnd;
             ExportType = settings.ExportType;
+            yAxisLogScale = settings.yAxisLogScale;
+            stackedBool = settings.stackedBool;
 
             ProductTypeToColor = ((ProductType[])Enum.GetValues(typeof(ProductType))).ToDictionary(p => p, p => DrawnSequence.ParseOxyColorFromName(settings.ProductTypeToColorValues[Array.IndexOf(((ProductType[])Enum.GetValues(typeof(ProductType))), p)]));
             BetaProductTypeToColor = ((ProductType[])Enum.GetValues(typeof(ProductType))).ToDictionary(p => p, p => DrawnSequence.ParseOxyColorFromName(settings.BetaProductTypeToColorValues[Array.IndexOf(((ProductType[])Enum.GetValues(typeof(ProductType))), p)]));
@@ -308,6 +315,8 @@ public static void ResetSettings()
             ExportType = "Pdf";
             UnannotatedPeakColor = OxyColors.LightGray;
             InternalIonColor = OxyColors.Purple;
+            yAxisLogScale = false;
+            stackedBool = true;
         }
 
         public static TValue GetValueOrDefault<TKey, TValue>(this IDictionary<TKey, TValue> dictionary, TKey key, TValue defaultValue)

GuiFunctions/MetaDraw/MetaDrawSettingsSnapshot.cs

@@ -30,6 +30,8 @@ public class MetaDrawSettingsSnapshot
         public List<string> CoverageTypeToColorValues { get; set; }
         public string UnannotatedPeakColor { get; set; }
         public string InternalIonColor { get; set; }
+        public bool yAxisLogScale { get; set; }
+        public bool stackedBool { get; set; }
 
         // filter settings
         public bool ShowDecoys { get; set; } = false;