// 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];
}