public static IFeatureAligner <MassTagDatabase, IEnumerable <UMCLight>, AlignmentData> CreateDatabaseAligner(
FeatureAlignmentType type,
LcmsWarpAlignmentOptions options,
SpectralOptions spectralOptions)
{
IFeatureAligner <MassTagDatabase, IEnumerable <UMCLight>, AlignmentData> aligner = null;
switch (type)
{
case FeatureAlignmentType.LCMS_WARP:
aligner = new LcmsWarpFeatureAligner(options);
break;
case FeatureAlignmentType.DIRECT_IMS_INFUSION:
aligner = new DummyAlignment();
break;
case FeatureAlignmentType.SPECTRAL_ALIGNMENT:
aligner = new SpectralAlignerWrapper {
Options = spectralOptions
};
break;
}
return(aligner);
}
public void TestAlignment(string datasetNameX, string datasetNameY)
{
var featureFileX = GetTestPath(datasetNameX + "_isos.csv");
var rawFileX = GetTestPath(datasetNameX + ".raw");
var featureFileY = GetTestPath(datasetNameY + "_isos.csv");
var rawFileY = GetTestPath(datasetNameY + ".raw");
Print("Detecting Features");
var featuresX = FindFeatures(rawFileX, featureFileX);
var featuresY = FindFeatures(rawFileY, featureFileY);
PrintFeatureMsMsData(featuresX);
PrintFeatureMsMsData(featuresY);
Print("Aligning Features");
// Align the features
var alignmentOptions = new AlignmentOptions();
var aligner = new LcmsWarpFeatureAligner(alignmentOptions.LCMSWarpOptions);
aligner.Align(featuresX, featuresY);
Print("");
Print("NET, NETAligned");
foreach (var feature in featuresY)
{
if (feature.HasMsMs())
{
Print(string.Format("{0}", feature.Net - feature.NetAligned));
}
}
}
public void TestPerformNetAlignment(string baselinePath, string aligneePath)
{
Console.WriteLine(@"I'm Testing!");
var rawBaselineData = File.ReadAllLines(baselinePath);
var rawFeaturesData = File.ReadAllLines(aligneePath);
var baseline = (from line in rawBaselineData
where line != ""
select line.Split(',')
into parsed
select new UMCLight
{
Net = Convert.ToDouble(parsed[0]),
ChargeState = Convert.ToInt32(parsed[1]),
Mz = Convert.ToDouble(parsed[2]),
ScanStart = Convert.ToInt32(parsed[3]),
Scan = Convert.ToInt32(parsed[3]),
MassMonoisotopic = Convert.ToDouble(parsed[4]),
MassMonoisotopicAligned = Convert.ToDouble(parsed[5]),
Id = Convert.ToInt32(parsed[6])
}).ToList();
var features = (from line in rawFeaturesData
where line != ""
select line.Split(',')
into parsed
select new UMCLight
{
Net = Convert.ToDouble(parsed[0]),
ChargeState = Convert.ToInt32(parsed[1]),
Mz = Convert.ToDouble(parsed[2]),
ScanStart = Convert.ToInt32(parsed[3]),
Scan = Convert.ToInt32(parsed[3]),
MassMonoisotopic = Convert.ToDouble(parsed[4]),
MassMonoisotopicAligned = Convert.ToDouble(parsed[5]),
Id = Convert.ToInt32(parsed[6])
}).ToList();
var oldStyle = new LcmsWarpFeatureAligner(new LcmsWarpAlignmentOptions());
var oldOutputData = oldStyle.Align(baseline, features);
Console.WriteLine(@"Done testing");
}
public static IFeatureAligner<IEnumerable<UMCLight>, IEnumerable<UMCLight>, classAlignmentData> CreateDatasetAligner(FeatureAlignmentType type,
LcmsWarpAlignmentOptions options,
SpectralOptions spectralOptions)
{
IFeatureAligner<IEnumerable<UMCLight>, IEnumerable<UMCLight>, classAlignmentData> aligner = null;
switch (type)
{
case FeatureAlignmentType.LCMS_WARP:
aligner = new LcmsWarpFeatureAligner {Options = options};
break;
case FeatureAlignmentType.DIRECT_IMS_INFUSION:
aligner = new DummyAlignment();
break;
case FeatureAlignmentType.SPECTRAL_ALIGNMENT:
aligner = new SpectralAlignerWrapper {Options = spectralOptions, Bandwidth = Bandwidth};
break;
}
return aligner;
}
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);
}
public void TestSpectralAlignment(string basePath, string baselineName, string aligneeName,
double comparisonCutoff)
{
RootDataPath = basePath;
var featureFileX = GetTestPath(baselineName + "_isos.csv");
var rawFileX = GetTestPath(baselineName + ".raw");
var featureFileY = GetTestPath(aligneeName + "_isos.csv");
var rawFileY = GetTestPath(aligneeName + ".raw");
Print("Detecting Features");
var baselineFeatures = FindFeatures(rawFileX, featureFileX);
var aligneeFeatures = FindFeatures(rawFileY, featureFileY);
Print("Aligning Features");
// Align the features
var aligner = new LcmsWarpFeatureAligner();
var alignmentOptions = new AlignmentOptions();
aligner.Options = alignmentOptions.LCMSWarpOptions;
aligner.Align(baselineFeatures, aligneeFeatures);
PrintFeatureMsMsData(baselineFeatures);
PrintFeatureMsMsData(aligneeFeatures);
var matches = GetSpectralMatches(
baselineFeatures, aligneeFeatures, comparisonCutoff);
Print(string.Format("Found {0} spectral matches", matches.Count));
Print("Similarity, Pre-Alignment, Post-Alignment");
var counts = new Dictionary<double, int>();
counts.Add(.9, 0);
counts.Add(.8, 0);
counts.Add(.7, 0);
counts.Add(.6, 0);
counts.Add(.5, 0);
var preDist = new List<double>();
var postDist = new List<double>();
foreach (var match in matches)
{
var baselineFeature = match.Baseline.ParentFeature.ParentFeature;
var aligneeFeature = match.Alignee.ParentFeature.ParentFeature;
var preAlignment = baselineFeature.Net - aligneeFeature.Net;
var postAlignment = baselineFeature.Net - aligneeFeature.NetAligned;
postDist.Add(postAlignment);
preDist.Add(preAlignment);
Print(string.Format("{0},{1},{2}", match.Similarity, preAlignment, postAlignment));
if (match.Similarity > .9)
{
counts[.9]++;
}
else if (match.Similarity > .8)
{
counts[.8]++;
}
else if (match.Similarity > .7)
{
counts[.7]++;
}
else if (match.Similarity > .6)
{
counts[.6]++;
}
}
Print("");
Print("Counts");
Print("");
foreach (var key in counts.Keys)
{
Print(string.Format("{0},{1}", key, counts[key]));
}
var test = new MannWhitneyTest();
var data = test.Test(preDist, postDist);
Print(string.Format("Two Tail - {0} ", data.TwoTail));
Print(string.Format("Left Tail - {0} ", data.LeftTail));
Print(string.Format("Right Tail - {0} ", data.RightTail));
}
public void TestAlignment(string datasetNameX, string datasetNameY)
{
var featureFileX = GetTestPath(datasetNameX + "_isos.csv");
var rawFileX = GetTestPath(datasetNameX + ".raw");
var featureFileY = GetTestPath(datasetNameY + "_isos.csv");
var rawFileY = GetTestPath(datasetNameY + ".raw");
Print("Detecting Features");
var featuresX = FindFeatures(rawFileX, featureFileX);
var featuresY = FindFeatures(rawFileY, featureFileY);
PrintFeatureMsMsData(featuresX);
PrintFeatureMsMsData(featuresY);
Print("Aligning Features");
// Align the features
var aligner = new LcmsWarpFeatureAligner();
var alignmentOptions = new AlignmentOptions();
aligner.Options = alignmentOptions.LCMSWarpOptions;
aligner.Align(featuresX, featuresY);
Print("");
Print("NET, NETAligned");
foreach (var feature in featuresY)
{
if (feature.HasMsMs())
{
Print(string.Format("{0}", feature.Net - feature.NetAligned));
}
}
}
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();
var baselineMs = UmcLoaderFactory.LoadMsFeatureData(path1);
var aligneeMs = UmcLoaderFactory.LoadMsFeatureData(path2);
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);
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);
}
public void TestSpectralAlignment(string basePath, string baselineName, string aligneeName,
double comparisonCutoff)
{
RootDataPath = basePath;
var featureFileX = GetTestPath(baselineName + "_isos.csv");
var rawFileX = GetTestPath(baselineName + ".raw");
var featureFileY = GetTestPath(aligneeName + "_isos.csv");
var rawFileY = GetTestPath(aligneeName + ".raw");
Print("Detecting Features");
var baselineFeatures = FindFeatures(rawFileX, featureFileX);
var aligneeFeatures = FindFeatures(rawFileY, featureFileY);
Print("Aligning Features");
// Align the features
var alignmentOptions = new AlignmentOptions();
var aligner = new LcmsWarpFeatureAligner(alignmentOptions.LCMSWarpOptions);
aligner.Align(baselineFeatures, aligneeFeatures);
PrintFeatureMsMsData(baselineFeatures);
PrintFeatureMsMsData(aligneeFeatures);
var matches = GetSpectralMatches(
baselineFeatures, aligneeFeatures, comparisonCutoff);
Print(string.Format("Found {0} spectral matches", matches.Count));
Print("Similarity, Pre-Alignment, Post-Alignment");
var counts = new Dictionary <double, int>();
counts.Add(.9, 0);
counts.Add(.8, 0);
counts.Add(.7, 0);
counts.Add(.6, 0);
counts.Add(.5, 0);
var preDist = new List <double>();
var postDist = new List <double>();
foreach (var match in matches)
{
var baselineFeature = match.Baseline.ParentFeature.GetParentFeature();
var aligneeFeature = match.Alignee.ParentFeature.GetParentFeature();
var preAlignment = baselineFeature.Net - aligneeFeature.Net;
var postAlignment = baselineFeature.Net - aligneeFeature.NetAligned;
postDist.Add(postAlignment);
preDist.Add(preAlignment);
Print(string.Format("{0},{1},{2}", match.Similarity, preAlignment, postAlignment));
if (match.Similarity > .9)
{
counts[.9]++;
}
else if (match.Similarity > .8)
{
counts[.8]++;
}
else if (match.Similarity > .7)
{
counts[.7]++;
}
else if (match.Similarity > .6)
{
counts[.6]++;
}
}
Print("");
Print("Counts");
Print("");
foreach (var key in counts.Keys)
{
Print(string.Format("{0},{1}", key, counts[key]));
}
var test = new MannWhitneyTest();
var data = test.Test(preDist, postDist);
Print(string.Format("Two Tail - {0} ", data.TwoTail));
Print(string.Format("Left Tail - {0} ", data.LeftTail));
Print(string.Format("Right Tail - {0} ", data.RightTail));
}
public void TestLcmsWarpAlignment(string path1, string path2, string svgPath)
{
// Convert relative paths to absolute paths
path1 = GetPath(path1);
path2 = GetPath(path2);
svgPath = GetPath(HEATMAP_RESULTS_FOLDER_BASE + svgPath);
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)
{
MaximumNetRange = .002
};
var baseline = finder.FindFeatures(baselineMs, options, null);
var alignee = finder.FindFeatures(aligneeMs, options, null);
var data = 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 = data.HeatScores;
var width = scores.GetLength(0);
var height = scores.GetLength(1);
heatMapSeries1.Data = new double[width, height];
for (var i = 0; i < width; i++)
{
for (var j = 0; j < height; j++)
{
heatMapSeries1.Data[i, j] = Convert.ToDouble(scores[i, j]);
}
}
plotModel1.Series.Add(heatMapSeries1);
var svg = new SvgExporter();
var svgString = svg.ExportToString(plotModel1);
using (var writer = File.CreateText(svgPath + ".svg"))
{
writer.Write(svgString);
}
}
public void TestLcmsWarpAlignment(string path1, string path2, string svgPath)
{
// Convert relative paths to absolute paths
path1 = GetPath(path1);
path2 = GetPath(path2);
svgPath = GetPath(HEATMAP_RESULTS_FOLDER_BASE + svgPath);
var aligner = new LcmsWarpFeatureAligner();
var baselineMs = UmcLoaderFactory.LoadMsFeatureData(path1);
var aligneeMs = UmcLoaderFactory.LoadMsFeatureData(path2);
var finder = FeatureFinderFactory.CreateFeatureFinder(FeatureFinderType.TreeBased);
var tolerances = new FeatureTolerances
{
FragmentationWindowSize = .5,
Mass = 13,
DriftTime = .3,
Net = .01
};
var options = new LcmsFeatureFindingOptions(tolerances)
{
MaximumNetRange = .002
};
var baseline = finder.FindFeatures(baselineMs, options, null);
var alignee = finder.FindFeatures(aligneeMs, options, null);
var data = 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 = data.heatScores;
var width = scores.GetLength(0);
var height = scores.GetLength(1);
heatMapSeries1.Data = new double[width, height];
for (var i = 0; i < width; i++)
{
for (var j = 0; j < height; j++)
{
heatMapSeries1.Data[i, j] = Convert.ToDouble(scores[i, j]);
}
}
plotModel1.Series.Add(heatMapSeries1);
var svg = new SvgExporter();
var svgString = svg.ExportToString(plotModel1);
using (var writer = File.CreateText(svgPath + ".svg"))
{
writer.Write(svgString);
}
}
public void TestPerformNetAlignment(string baselinePath, string aligneePath)
{
Console.WriteLine(@"I'm Testing!");
var rawBaselineData = File.ReadAllLines(baselinePath);
var rawFeaturesData = File.ReadAllLines(aligneePath);
var baseline = (from line in rawBaselineData
where line != ""
select line.Split(',')
into parsed
select new UMCLight
{
Net = Convert.ToDouble(parsed[0]),
ChargeState = Convert.ToInt32(parsed[1]),
Mz = Convert.ToDouble(parsed[2]),
ScanStart = Convert.ToInt32(parsed[3]),
Scan = Convert.ToInt32(parsed[3]),
MassMonoisotopic = Convert.ToDouble(parsed[4]),
MassMonoisotopicAligned = Convert.ToDouble(parsed[5]),
Id = Convert.ToInt32(parsed[6])
}).ToList();
var features = (from line in rawFeaturesData
where line != ""
select line.Split(',')
into parsed
select new UMCLight
{
Net = Convert.ToDouble(parsed[0]),
ChargeState = Convert.ToInt32(parsed[1]),
Mz = Convert.ToDouble(parsed[2]),
ScanStart = Convert.ToInt32(parsed[3]),
Scan = Convert.ToInt32(parsed[3]),
MassMonoisotopic = Convert.ToDouble(parsed[4]),
MassMonoisotopicAligned = Convert.ToDouble(parsed[5]),
Id = Convert.ToInt32(parsed[6])
}).ToList();
var oldStyle = new LcmsWarpFeatureAligner();
var oldOutputData = oldStyle.Align(baseline, features);
Console.WriteLine(@"Done testing");
}
public void TestLcmsWarpPortCpp(string relativeBaselinePath, string relativeAligneePath, string relativeOutput, string name)
{
var 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;
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);
}
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);
}
