// 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 AlignmentPlotCreator(AlignmentData alignment) { var residuals = alignment.ResidualData; Heatmap = HeatmapFactory.CreateAlignedHeatmap(alignment.HeatScores, alignment.BaselineIsAmtDB); NetResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Net, residuals.LinearCustomNet, residuals.LinearNet, "NET Residuals", "Scans", "NET"); MassHistogram = HistogramFactory.CreateHistogram(alignment.MassErrorHistogram, "Mass Error", "Mass Error (ppm)"); NetHistogram = HistogramFactory.CreateHistogram(alignment.NetErrorHistogram, "NET Error", "NET Error"); MassMzResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Mz, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "m/z", "Mass Errors"); MassScanResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Net, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "Scan", "Mass Errors"); }
/// <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(); }
private static void TestNow(string relativeBaselinePath, string relativeAligneePath, string relativeOutput, string name) { string baselinePath = GetPath(relativeBaselinePath); var aligneePath = GetPath(relativeAligneePath); var aligner = new LcmsWarpFeatureAligner(); var rawBaselineData = File.ReadAllLines(baselinePath); var rawFeaturesData = File.ReadAllLines(aligneePath); var outputPath = GetOutputPath(relativeOutput); var delimiter = new[] { TextDelimiter }; if (!Directory.Exists(outputPath)) { Directory.CreateDirectory(outputPath); } var baseline = (from line in rawBaselineData where line != "" select line.Split(delimiter, StringSplitOptions.RemoveEmptyEntries) into parsed select new UMCLight { Net = Convert.ToDouble(parsed[0]), ChargeState = Convert.ToInt32(parsed[1]), Mz = Convert.ToDouble(parsed[2]), Scan = Convert.ToInt32(parsed[3]), MassMonoisotopic = Convert.ToDouble(parsed[4]), MassMonoisotopicAligned = Convert.ToDouble(parsed[5]), Id = Convert.ToInt32(parsed[6]), ScanStart = Convert.ToInt32(parsed[7]), ScanEnd = Convert.ToInt32(parsed[8]), ScanAligned = Convert.ToInt32(parsed[9]) }).ToList(); var features = (from line in rawFeaturesData where line != "" select line.Split(delimiter, StringSplitOptions.RemoveEmptyEntries) into parsed select new UMCLight { Net = Convert.ToDouble(parsed[0]), ChargeState = Convert.ToInt32(parsed[1]), Mz = Convert.ToDouble(parsed[2]), Scan = Convert.ToInt32(parsed[3]), MassMonoisotopic = Convert.ToDouble(parsed[4]), MassMonoisotopicAligned = Convert.ToDouble(parsed[5]), Id = Convert.ToInt32(parsed[6]), ScanStart = Convert.ToInt32(parsed[7]), ScanEnd = Convert.ToInt32(parsed[8]), ScanAligned = Convert.ToInt32(parsed[9]) }).ToList(); var maxd = features.Max(x => x.Net); var mind = features.Min(x => x.Net); if (maxd - mind < double.Epsilon) { throw new Exception("There is something wrong with the features NET values"); } aligner.Options.AlignType = AlignmentType.NET_MASS_WARP; var outputData = aligner.Align(baseline, features); var residuals = outputData.ResidualData; using (var writer = new StreamWriter(@"E:\MultiAlignTest\Results\heat-scores-old.txt")) { foreach (var oovarscore in outputData.heatScores) { writer.WriteLine(oovarscore); } } var heatmap = HeatmapFactory.CreateAlignedHeatmap(outputData.heatScores); var netHistogram = HistogramFactory.CreateHistogram(outputData.netErrorHistogram, "NET Error Histogram", "NET Error"); var massHistogram = HistogramFactory.CreateHistogram(outputData.massErrorHistogram, "Mass Error Histogram", "Mass Error (ppm)"); var netResidual = ScatterPlotFactory.CreateResidualPlot(residuals.Scan, 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.Scan, residuals.MzMassError, residuals.MzMassErrorCorrected, "Mass Residuals", "Scan", "Mass Errors"); var directory = Path.Combine(outputPath, name); var encoder = new SvgEncoder(); PlotImageUtility.SaveImage(heatmap, directory + "_heatmap.svg", encoder); PlotImageUtility.SaveImage(netResidual, directory + "_netResidual.svg", encoder); PlotImageUtility.SaveImage(massMzResidual, directory + "_massMzResidual.svg", encoder); PlotImageUtility.SaveImage(massScanResidual, directory + "_massScanResidual.svg", encoder); //PlotImageUtility.SaveImage(netHistogram, directory + "_netHistogram.svg", encoder); PlotImageUtility.SaveImage(massHistogram, directory + "_massHistogram.svg", encoder); }
public void TestLcmsWarpPort(string relativeBaselinePath, string relativeAligneePath, string relativeOutput, string name) { var baselinePath = GetPath(relativeBaselinePath); var aligneePath = GetPath(relativeAligneePath); var options = new LcmsWarpAlignmentOptions { AlignType = LcmsWarpAlignmentType.NET_MASS_WARP, CalibrationType = LcmsWarpCalibrationType.Both }; var aligner = new LcmsWarpFeatureAligner(options); var rawBaselineData = File.ReadAllLines(baselinePath); var rawFeaturesData = File.ReadAllLines(aligneePath); var outputPath = GetOutputPath(relativeOutput); var delimiter = new[] { TextDelimiter }; if (!Directory.Exists(outputPath)) { Directory.CreateDirectory(outputPath); } var baseline = (from line in rawBaselineData where line != "" select line.Split(delimiter, StringSplitOptions.RemoveEmptyEntries) into parsed select new UMCLight { Net = Convert.ToDouble(parsed[0]), ChargeState = Convert.ToInt32(parsed[1]), Mz = Convert.ToDouble(parsed[2]), Scan = Convert.ToInt32(parsed[3]), MassMonoisotopic = Convert.ToDouble(parsed[4]), MassMonoisotopicAligned = Convert.ToDouble(parsed[5]), Id = Convert.ToInt32(parsed[6]), ScanStart = Convert.ToInt32(parsed[7]), ScanEnd = Convert.ToInt32(parsed[8]), ScanAligned = Convert.ToInt32(parsed[9]) }).ToList(); var features = (from line in rawFeaturesData where line != "" select line.Split(delimiter, StringSplitOptions.RemoveEmptyEntries) into parsed select new UMCLight { Net = Convert.ToDouble(parsed[0]), ChargeState = Convert.ToInt32(parsed[1]), Mz = Convert.ToDouble(parsed[2]), Scan = Convert.ToInt32(parsed[3]), MassMonoisotopic = Convert.ToDouble(parsed[4]), MassMonoisotopicAligned = Convert.ToDouble(parsed[5]), Id = Convert.ToInt32(parsed[6]), ScanStart = Convert.ToInt32(parsed[7]), ScanEnd = Convert.ToInt32(parsed[8]), ScanAligned = Convert.ToInt32(parsed[9]) }).ToList(); var outputData = aligner.Align(baseline, features); var residuals = outputData.ResidualData; var heatmap = HeatmapFactory.CreateAlignedHeatmap(outputData.HeatScores, false); var netHistogram = HistogramFactory.CreateHistogram(outputData.NetErrorHistogram, "NET Error", "NET Error"); var massHistogram = HistogramFactory.CreateHistogram(outputData.MassErrorHistogram, "Mass Error", "Mass Error (ppm)"); 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 directory = Path.Combine(outputPath, name); var encoder = new SvgEncoder(); PlotImageUtility.SaveImage(heatmap, directory + "_heatmap.svg", encoder); PlotImageUtility.SaveImage(netResidual, directory + "_netResidual.svg", encoder); PlotImageUtility.SaveImage(massMzResidual, directory + "_massMzResidual.svg", encoder); PlotImageUtility.SaveImage(massScanResidual, directory + "_massScanResidual.svg", encoder); PlotImageUtility.SaveImage(netHistogram, directory + "_netHistogram.svg", encoder); PlotImageUtility.SaveImage(massHistogram, directory + "_massHistogram.svg", encoder); }