private IList <UMCLight> AlignDataset(
IList <UMCLight> features,
IEnumerable <UMCLight> baselineFeatures,
MassTagDatabase database,
DatasetInformation datasetInfo,
DatasetInformation baselineInfo)
{
AlignmentData alignmentData;
if (baselineInfo == null && database == null)
{
throw new NullReferenceException("No reference was set for LC-MS alignment.");
}
// align the data.
if (baselineFeatures != null && baselineInfo != null && baselineInfo.IsBaseline)
{
// Align pairwise and cache results intermediately.
var aligner = m_algorithms.DatasetAligner;
RegisterProgressNotifier(aligner);
UpdateStatus("Aligning " + datasetInfo.DatasetName + " to baseline.");
alignmentData = aligner.Align(baselineFeatures, features);
DeRegisterProgressNotifier(aligner);
}
else
{
// Align pairwise and cache results intermediately.
var aligner = m_algorithms.DatabaseAligner;
RegisterProgressNotifier(aligner);
UpdateStatus("Aligning " + datasetInfo.DatasetName + " to mass tag database.");
alignmentData = aligner.Align(database, features);
DeRegisterProgressNotifier(aligner);
}
if (alignmentData != null)
{
alignmentData.AligneeDataset = datasetInfo.DatasetName;
alignmentData.DatasetID = datasetInfo.DatasetId;
}
var args = new FeaturesAlignedEventArgs(datasetInfo,
baselineFeatures,
features,
alignmentData);
if (FeaturesAligned != null)
{
FeaturesAligned(this, args);
}
UpdateStatus("Updating cache with aligned features.");
return(features);
}
public void CreateAlignmentPlots(FeaturesAlignedEventArgs e)
{
Action workAction = () =>
{
BuildAlignmentPlotView(e);
Reporter.CreateAlignmentPlots(e);
};
ThreadSafeDispatcher.Invoke(workAction);
}
/// <summary>
/// Builds the alignment plot views.
/// </summary>
/// <param name="e"></param>
private void BuildAlignmentPlotView(FeaturesAlignedEventArgs e)
{
var view = new AlignmentPlotView {
AlignmentData = e
};
GalleryImages.Insert(0, view);
if (GalleryImages.Count > 10)
{
GalleryImages.RemoveAt(0);
}
}
/// <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();
}
