/// <summary>
/// Creates the final analysis plots.
/// </summary>
public void CreateChargePlots(Dictionary <int, int> chargeMap)
{
Logger.PrintMessage("Creating Charge State Plots");
var report = Config.Report;
report.PushTextHeader("Cluster Charge States");
report.PushStartTable();
var path = Path.Combine(Config.AnalysisPath, PlotPath, "clusters_chargestates.png");
var histogram = HistogramFactory.CreateHistogram(chargeMap, "Charge States", "Charge States");
PlotImageUtility.SaveImage(histogram, path);
report.PushImageColumn(path);
report.PushEndTable();
}
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");
}
public void CreateClusterPlots(FeaturesClusteredEventArgs args)
{
// Plots:
// Dataset member
// Total members
// Cluster scatter plot
var clusters = args.Clusters;
var report = Config.Report;
Logger.PrintMessage("Creating Charge State Plots");
report.PushStartTable();
report.PushStartTableRow();
report.PushTextHeader("Cluster Statistics");
report.PushEndTableRow();
report.PushStartTableRow();
var path = Path.Combine(Config.AnalysisPath, PlotPath, "clusters_scatterplot.png");
var clusterScatterPlot = ScatterPlotFactory.CreateClusterMassScatterPlot(clusters);
PlotImageUtility.SaveImage(clusterScatterPlot, path);
report.PushImageColumn(path, WIDTH, HEIGHT);
report.PushEndTableRow();
report.PushStartTableRow();
path = Path.Combine(Config.AnalysisPath, PlotPath, "clusters_datasetMembersHistogram.png");
var datasetMemberHistogram =
HistogramFactory.CreateHistogram(clusters.CreateClusterDatasetMemberSizeHistogram(), "Dataset Members", "Dataset Count");
PlotImageUtility.SaveImage(datasetMemberHistogram, path);
report.PushImageColumn(path, WIDTH, HEIGHT);
path = Path.Combine(Config.AnalysisPath, PlotPath, "clusters_clusterSizeHistogram.png");
var clusterSizeHistogram = HistogramFactory.CreateHistogram(clusters.CreateClusterSizeHistogram(), "Cluster Members", "Cluster Size");
PlotImageUtility.SaveImage(clusterSizeHistogram, path);
report.PushImageColumn(path, WIDTH, HEIGHT);
report.PushEndTableRow();
report.PushEndTable();
}
/// <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();
}
public void TestMsFeatureScatterPlot(string path1, string path2, string pngPath)
{
// Convert relative paths to absolute paths
path1 = GetPath(path1);
path2 = GetPath(path2);
pngPath = GetPath(pngPath);
var fiOutput = new FileInfo(pngPath);
var didirectory = fiOutput.Directory;
if (didirectory == null)
{
throw new DirectoryNotFoundException(pngPath);
}
if (!didirectory.Exists)
{
didirectory.Create();
}
var aligner = new LcmsWarpFeatureAligner(new LcmsWarpAlignmentOptions());
var isosFilterOptions = new DeconToolsIsosFilterOptions();
var baselineMs = UmcLoaderFactory.LoadMsFeatureData(path1, isosFilterOptions);
var aligneeMs = UmcLoaderFactory.LoadMsFeatureData(path2, isosFilterOptions);
var finder = FeatureFinderFactory.CreateFeatureFinder(FeatureFinderType.TreeBased);
var tolerances = new FeatureTolerances
{
FragmentationWindowSize = .5,
Mass = 13,
DriftTime = .3,
Net = .01
};
var options = new LcmsFeatureFindingOptions(tolerances);
options.MaximumNetRange = .002;
var baseline = finder.FindFeatures(baselineMs, options, null);
var alignee = finder.FindFeatures(aligneeMs, options, null);
var alignmentResults = aligner.Align(baseline, alignee);
var plotModel1 = new PlotModel
{
Subtitle = "Interpolated, cartesian axes",
Title = "HeatMapSeries"
};
var palette = OxyPalettes.Hot(200);
var linearColorAxis1 = new LinearColorAxis
{
InvalidNumberColor = OxyColors.Gray,
Position = AxisPosition.Right,
Palette = palette
};
plotModel1.Axes.Add(linearColorAxis1);
// linearColorAxis1.
var linearAxis1 = new LinearAxis {
Position = AxisPosition.Bottom
};
plotModel1.Axes.Add(linearAxis1);
var linearAxis2 = new LinearAxis();
plotModel1.Axes.Add(linearAxis2);
var heatMapSeries1 = new HeatMapSeries
{
X0 = 0,
X1 = 1,
Y0 = 0,
Y1 = 1,
FontSize = .2
};
var scores = alignmentResults.HeatScores;
var width = scores.GetLength(0);
var height = scores.GetLength(1);
heatMapSeries1.Data = new double[width, height];
var seriesData = heatMapSeries1.Data;
for (var i = 0; i < width; i++)
{
for (var j = 0; j < height; j++)
{
seriesData[i, j] = Convert.ToDouble(scores[i, j]);
}
}
plotModel1.Series.Add(heatMapSeries1);
var svg = new SvgExporter();
var svgString = svg.ExportToString(plotModel1);
var xml = new XmlDocument();
xml.LoadXml(svgString);
var x = SvgDocument.Open(xml); // Svg.SvgDocument();
var bmp = x.Draw();
bmp.Save(pngPath);
var heatmap = HeatmapFactory.CreateAlignedHeatmap(alignmentResults.HeatScores, false);
var netHistogram = HistogramFactory.CreateHistogram(alignmentResults.NetErrorHistogram, "NET Error", "NET Error");
var massHistogram = HistogramFactory.CreateHistogram(alignmentResults.MassErrorHistogram, "Mass Error", "Mass Error (ppm)");
var baseName = Path.Combine(didirectory.FullName, Path.GetFileNameWithoutExtension(fiOutput.Name));
var encoder = new SvgEncoder();
PlotImageUtility.SaveImage(heatmap, baseName + "_heatmap.svg", encoder);
PlotImageUtility.SaveImage(netHistogram, baseName + "_netHistogram.svg", encoder);
PlotImageUtility.SaveImage(massHistogram, baseName + "_massHistogram.svg", encoder);
}
/// <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);
}