// Using a DependencyProperty as the backing store for MassMzImage. This enables animation, styling, binding, etc... private void CreatePlots() { if (AlignmentData == null || AlignmentData.AlignmentData == null) { return; } var alignmentData = AlignmentData.AlignmentData; var heatmap = HeatmapFactory.CreateAlignedHeatmap(alignmentData.HeatScores, alignmentData.BaselineIsAmtDB); var feature = ScatterPlotFactory.CreateFeatureMassScatterPlot(AlignmentData.AligneeFeatures); var netHistogram = HistogramFactory.CreateHistogram(alignmentData.NetErrorHistogram, "NET Error", "NET Error"); var massHistogram = HistogramFactory.CreateHistogram(alignmentData.NetErrorHistogram, "Mass Error", "Mass Error (ppm)"); var residuals = alignmentData.ResidualData; var netResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Net, residuals.LinearCustomNet, residuals.LinearNet, "NET Residuals", "Scans", "NET"); var massMzResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Mz, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "m/z", "Mass Errors"); var massScanResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Net, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "Scan", "Mass Errors"); NetScanImage = ImageConverter.ConvertImage(PlotImageUtility.CreateImage(netResidual)); MassHistogram = ImageConverter.ConvertImage(PlotImageUtility.CreateImage(massHistogram)); NetHistogram = ImageConverter.ConvertImage(PlotImageUtility.CreateImage(netHistogram)); HeatmapImage = ImageConverter.ConvertImage(PlotImageUtility.CreateImage(heatmap)); MassMzImage = ImageConverter.ConvertImage(PlotImageUtility.CreateImage(massMzResidual)); MassScanImage = ImageConverter.ConvertImage(PlotImageUtility.CreateImage(massScanResidual)); FeaturePlotImage = ImageConverter.ConvertImage(PlotImageUtility.CreateImage(feature)); }
public FeaturesViewModel(IEnumerable <UMCLight> features, string text) { Text = text; Height = 800; Width = 800; FeaturesModel = ScatterPlotFactory.CreateFeatureMassScatterPlot(features); }
private void CreateMassTagPlots() { var data = MassTagsData; PlotName = string.Format("Mass Tag Database"); var plot = ScatterPlotFactory.CreateFeatureMassScatterPlot(data.MassTags); plot.Model.Title = PlotName; FeaturesImage = ImageConverter.ConvertImage(PlotImageUtility.CreateImage(plot)); }
public void CreateMassTagPlot(MassTagsLoadedEventArgs e) { Logger.PrintMessage("Creating Mass Tag Plot."); if (e.Database == null) { return; } if (e.MassTags == null) { return; } var feature = ScatterPlotFactory.CreateFeatureMassScatterPlot(e.MassTags); var name = e.Database.Name; var directory = Path.Combine(Config.AnalysisPath, name); PlotImageUtility.SaveImage(feature, directory + "_mtdb.png"); }
/// <summary> /// Creates images for the HTML output for baseline data /// </summary> /// <param name="e"></param> public void CreateBaselinePlots(BaselineFeaturesLoadedEventArgs e) { var baselineInfo = e.DatasetInformation; if (baselineInfo == null) { return; } var feature = ScatterPlotFactory.CreateFeatureMassScatterPlot(e.Features); var name = e.DatasetInformation.DatasetName; var directory = Path.Combine(Config.AnalysisPath, PlotPath, name); var report = Config.Report; report.PushTextHeader("Baseline Features"); report.PushStartTableRow(); Config.Report.PushImageColumn(directory + "_features.png", WIDTH, HEIGHT); PlotImageUtility.SaveImage(feature, directory + "_features.png"); report.PushEndTableRow(); }
/// private void CreatePlots() { var data = BaselineData; var name = ""; if (data.DatasetInformation == null) { if (data.Database != null) { name = data.Database.Name; } } else { name = data.DatasetInformation.DatasetName; } PlotName = string.Format("Baseline: {0}", name); var plot = ScatterPlotFactory.CreateFeatureMassScatterPlot(data.Features); FeaturesImage = ImageConverter.ConvertImage(PlotImageUtility.CreateImage(plot)); }
/// <summary> /// Creates alignment plots for the HTML output. /// </summary> public void CreateAlignmentPlots(FeaturesAlignedEventArgs e) { var name = e.AligneeDatasetInformation.DatasetName; var alignmentData = e.AlignmentData; if (alignmentData == null) { return; } var directory = Path.Combine(Config.AnalysisPath, PlotPath, name); var heatmap = HeatmapFactory.CreateAlignedHeatmap(alignmentData.HeatScores, alignmentData.BaselineIsAmtDB); var feature = ScatterPlotFactory.CreateFeatureMassScatterPlot(e.AligneeFeatures); var netHistogram = HistogramFactory.CreateHistogram(alignmentData.NetErrorHistogram, "NET Error", "NET Error"); var massHistogram = HistogramFactory.CreateHistogram(alignmentData.MassErrorHistogram, "Mass Error", "Mass Error (ppm)"); var residuals = alignmentData.ResidualData; var netResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Net, residuals.LinearCustomNet, residuals.LinearNet, "NET Residuals", "Scans", "NET"); var massMzResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Mz, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "m/z", "Mass Errors"); var massScanResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Net, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "Scan", "Mass Errors"); var report = Config.Report; report.PushLargeText(string.Format("Alignee Statistics - {0}", name)); report.PushStartTable(); // Features report.PushStartTableRow(); report.PushTextHeader("Features"); report.PushEndTableRow(); report.PushStartTableRow(); Config.Report.PushImageColumn(directory + "_features.png", WIDTH, HEIGHT); Config.Report.PushImageColumn(directory + "_heatmap.png", WIDTH, HEIGHT); PlotImageUtility.SaveImage(feature, directory + "_features.png"); PlotImageUtility.SaveImage(heatmap, directory + "_heatmap.png"); report.PushEndTableRow(); // Histograms report.PushStartTableRow(); report.PushTextHeader("Histograms"); report.PushEndTableRow(); report.PushStartTableRow(); Config.Report.PushImageColumn(directory + "_netHistogram.png"); Config.Report.PushImageColumn(directory + "_massHistogram.png"); PlotImageUtility.SaveImage(netHistogram, directory + "_netHistogram.png"); PlotImageUtility.SaveImage(massHistogram, directory + "_massHistogram.png"); report.PushEndTableRow(); // Residuals report.PushStartTableRow(); report.PushTextHeader("Histograms"); report.PushEndTableRow(); report.PushStartTableRow(); Config.Report.PushImageColumn(directory + "_netResidual.png"); Config.Report.PushImageColumn(directory + "_massMzResidual.png"); Config.Report.PushImageColumn(directory + "_massScanResidual.png"); PlotImageUtility.SaveImage(netResidual, directory + "_netResidual.png"); PlotImageUtility.SaveImage(massMzResidual, directory + "_massMzResidual.png"); PlotImageUtility.SaveImage(massScanResidual, directory + "_massScanResidual.png"); report.PushEndTableRow(); report.PushEndTable(); }
/// <summary> /// Updates the plots with data stored in the cache. /// </summary> private void UpdatePlotsWithClusterData(UMCClusterLightMatched matchedCluster) { //TODO: Make this select mass! ClusterMassPlot = ScatterPlotFactory.CreateFeatureMassScatterPlot(matchedCluster.Cluster.Features); //TODO: Make this select drift time! ClusterDriftPlot = ScatterPlotFactory.CreateFeatureDriftTimeScatterPlot(matchedCluster.Cluster.Features); var cluster = matchedCluster.Cluster; // Then we find all the nearby clusters var massPpm = ClusterTolerances.Mass; var net = ClusterTolerances.Net; //TODO: Add other clusters back // var minMass = FeatureLight.ComputeDaDifferenceFromPPM(cluster.MassMonoisotopic, massPpm); //var maxMass = FeatureLight.ComputeDaDifferenceFromPPM(cluster.MassMonoisotopic, -massPpm); //var minNet = cluster.Net - net; //var maxNet = cluster.Net + net; //var otherClusters // = SingletonDataProviders.Providers.ClusterCache.FindNearby(minMass, maxMass, minNet, maxNet); //// Remove self from the list //var index = otherClusters.FindIndex(x => x.Id == cluster.Id); //if (index > -1) //{ // otherClusters.RemoveAt(index); //} //// Then find the matching clusters and map them back to previously matched (to mass tag data) //var otherClusterMatches = new List<UMCClusterLightMatched>(); //otherClusters.ForEach(x => otherClusterMatches.Add(FeatureCacheManager<UMCClusterLightMatched>.FindById(x.Id))); //foreach (var matchedOtherCluster in otherClusterMatches) //{ // matchedOtherCluster.Cluster.Features.Clear(); // matchedOtherCluster.Cluster.ReconstructUMCCluster(SingletonDataProviders.Providers, false, false); //} // Map out the MS/MS spectra. var msmsFeatures = new List <MSFeatureMsMs>(); foreach (var feature in cluster.Features) { foreach (var msFeature in feature.MsFeatures) { msmsFeatures.AddRange(msFeature.MSnSpectra.Select(spectrum => new MSFeatureMsMs { FeatureID = msFeature.Id, FeatureGroupID = msFeature.GroupId, Mz = msFeature.Mz, PrecursorMZ = spectrum.PrecursorMz, FeatureScan = msFeature.Scan, MsMsScan = spectrum.Scan, MassMonoisotopicAligned = msFeature.MassMonoisotopicAligned, ChargeState = msFeature.ChargeState, Sequence = "", PeptideSequence = "" })); } } var features = new List <UMCLight>(); features.AddRange(matchedCluster.Cluster.Features); Features.Clear(); features.ForEach(x => Features.Add(new UMCTreeViewModel(x))); SelectedFeature = Features[0]; }