public ZedGraphITraqSpectrum(ZedGraphControl zgcGraph, Graphics g, string title)
{
this.zgcGraph = zgcGraph;
zgcGraph.InitMasterPanel(g, 2, title, PaneLayout.SingleColumn);
scanItraq = new ZedGraphScanITraq(zgcGraph, zgcGraph.MasterPane[0], false);
isolationWindow = new ZedGraphScanIsolationWindow(zgcGraph, zgcGraph.MasterPane[1]);
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public MatchImageBuilder(string mgfFile, string targetDir)
{
var mgfReader = new Mascot.MascotGenericFormatReader <MatchedPeak>();
var spectra = mgfReader.ReadFromFile(mgfFile);
spectra.ForEach(m => m.Experimental = m.Experimental.Substring(0, m.Experimental.Length - 4));
mgfMap = spectra.ToDictionary(m => string.Format("{0}_{1}", m.Experimental, m.ScanTimes[0].Scan));
var mods = new Dictionary <char, double>();
mods['&'] = 7.017166;
mods['#'] = 3.010071;
mods['@'] = 6.013809;
mods['*'] = 15.994919;
mods['C'] = 57.021464 + aas['C'].MonoMass; // 160.16523;
mods['K'] = 8.014206 + aas['K'].MonoMass;
mods['R'] = 10.008270 + aas['R'].MonoMass;
aas.SetModification(mods);
yBuilder = new CIDPeptideYSeriesBuilder <MatchedPeak>()
{
CurAminoacids = aas
};
bBuilder = new CIDPeptideBSeriesBuilder <MatchedPeak>()
{
CurAminoacids = aas
};
y2Builder = new CIDPeptideY2SeriesBuilder <MatchedPeak>()
{
CurAminoacids = aas
};
b2Builder = new CIDPeptideB2SeriesBuilder <MatchedPeak>()
{
CurAminoacids = aas
};
zgcPeaks = new ZedGraphControl();
zgcPeaks.Width = 1600;
zgcPeaks.Height = 1200;
zgcPeaks.MasterPane.Border.IsVisible = false;
zgcPeaks.InitMasterPanel(Graphics.FromImage(zgcPeaks.GetImage()), 2, "");
zgcPeaks.IsSynchronizeXAxes = true;
if (!Directory.Exists(targetDir))
{
Directory.CreateDirectory(targetDir);
}
this.targetDir = targetDir;
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
var spectra = e.Item as IEnumerable <IIdentifiedSpectrum>;
if (spectra == null)
{
throw new ArgumentException("e.Item should be IEnumerable<IIdentifiedSpectrum>");
}
var validItems = (from spectrum in spectra
let item = spectrum.FindIsobaricItem()
where null != item
select item).ToList();
zgcGraph.InitMasterPanel(g, validItems.Count, title, this.pl);
for (int i = 0; i < validItems.Count; i++)
{
new ZedGraphScanITraq(zgcGraph, zgcGraph.MasterPane[i], false).Update(sender, new UpdateQuantificationItemEventArgs(null, validItems[i]));
}
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
ITraqProteinStatisticOption option = e.Option as ITraqProteinStatisticOption;
IIdentifiedProteinGroup protein = null;
if (e.Item is IEnumerable <IIdentifiedSpectrum> )
{
var spectra = e.Item as IEnumerable <IIdentifiedSpectrum>;
protein = new IdentifiedProteinGroup();
protein.Add(new IdentifiedProtein());
protein[0].Peptides.AddRange(from s in spectra select s.Peptide);
}
else if (e.Item is IIdentifiedProteinGroup)
{
protein = e.Item as IIdentifiedProteinGroup;
}
if (protein == null)
{
throw new ArgumentException("e.Item should be IIdentifiedProteinGroup or IEnumerable<IIdentifiedSpectrum>");
}
var validItem = protein[0].Peptides.FirstOrDefault(m =>
{
var item = m.Spectrum.FindIsobaricItem();
return(null != item && item.Valid);
});
if (null == validItem)
{
zgcGraph.ClearData(true);
return;
}
var masterPane = zgcGraph.InitMasterPanel(g, 1, title, this.pl);
var panel = masterPane[0];
var samples = option.GetSamples(validItem.Spectrum.FindIsobaricItem().PlexType);
var dsNames = option.DatasetMap.Keys.OrderBy(m => m).ToList();
var ratioCalc = option.GetRatioCalculator();
xlabels.Clear();
double index = 0.0;
string outlierStr = "Outlier";
string proteinStr = "Protein Ratio";
foreach (var dsName in dsNames)
{
var expNames = new HashSet <string>(option.DatasetMap[dsName]);
foreach (var sample in samples)
{
index += 1.0;
ratioCalc.GetSample = sample.GetValue;
ratioCalc.DatasetName = dsName;
ratioCalc.ChannelName = sample.ChannelRatioName;
ratioCalc.Filter = m => expNames.Contains(m.Query.FileScan.Experimental);
var ratios = ratioCalc.Calculate(protein);
xlabels.Add(dsName + ":" + sample.Name);
if (ratios.Count > 0)
{
var ratio = protein[0].FindITraqChannelItem(dsName, sample.ChannelRatioName).Ratio;
PointPairList pplNormal = new PointPairList();
PointPairList pplOutlier = new PointPairList();
PointPairList pplProteinRatio = new PointPairList();
foreach (var r in ratios)
{
if (r.IsOutlier)
{
pplOutlier.Add(new PointPair(index, Math.Log(r.Ratio)));
}
else
{
pplNormal.Add(new PointPair(index, Math.Log(r.Ratio)));
}
}
pplProteinRatio.Add(new PointPair(index, Math.Log(ratio)));
panel.AddPoints(pplProteinRatio, Color.Red, proteinStr);
if (pplOutlier.Count > 0)
{
panel.AddPoints(pplOutlier, Color.Green, outlierStr);
outlierStr = string.Empty;
}
panel.AddPoints(pplNormal, Color.Black);
proteinStr = string.Empty;
}
}
}
panel.XAxis.ScaleFormatEvent += new Axis.ScaleFormatHandler(XAxis_ScaleFormatEvent);
panel.XAxis.Scale.Min = 0.0;
panel.XAxis.Scale.Max = index + 1.0;
panel.XAxis.Scale.FontSpec.Angle = 90;
panel.YAxis.Title.Text = "log(Ratio)";
ZedGraphicExtension.UpdateGraph(zgcGraph);
}
public void Update(object sender, UpdateQuantificationItemEventArgs e)
{
ITraqProteinStatisticOption option = e.Option as ITraqProteinStatisticOption;
IIdentifiedProteinGroup protein = null;
if (e.Item is IEnumerable <IIdentifiedSpectrum> )
{
var spectra = e.Item as IEnumerable <IIdentifiedSpectrum>;
protein = new IdentifiedProteinGroup();
protein.Add(new IdentifiedProtein());
protein[0].Peptides.AddRange(from s in spectra select s.Peptide);
}
else if (e.Item is IIdentifiedProteinGroup)
{
protein = e.Item as IIdentifiedProteinGroup;
}
if (protein == null)
{
throw new ArgumentException("e.Item should be IIdentifiedProteinGroup or IEnumerable<IIdentifiedSpectrum>");
}
var validItem = protein[0].Peptides.FirstOrDefault(m =>
{
var item = m.Spectrum.FindIsobaricItem();
return(null != item && item.Valid);
});
if (null == validItem)
{
zgcGraph.ClearData(true);
return;
}
var masterPane = zgcGraph.InitMasterPanel(g, 1, title, this.pl);
var panel = masterPane[0];
var samples = option.GetSamples(validItem.Spectrum.FindIsobaricItem().PlexType);
var dsNames = option.DatasetMap.Keys.OrderBy(m => m).ToList();
var ratioCalc = option.GetRatioCalculator();
List <string> xlabels = new List <string>();
List <PointPairList> outliers = new List <PointPairList>();
List <PointPairList> normals = new List <PointPairList>();
PointPairList proteins = new PointPairList();
//按照数据集循环
foreach (var dsName in dsNames)
{
var expNames = new HashSet <string>(option.DatasetMap[dsName]);
//按照样品循环
foreach (var sample in samples)
{
ratioCalc.GetSample = sample.GetValue;
ratioCalc.DatasetName = dsName;
ratioCalc.ChannelName = sample.ChannelRatioName;
ratioCalc.Filter = m => expNames.Contains(m.Query.FileScan.Experimental);
var ratios = ratioCalc.Calculate(protein);
//添加相应的分类名
xlabels.Add(dsName + ":" + sample.Name);
//每个分类有三种数据：outlier,normal和proteinratio
var outlier = new PointPairList();
outliers.Add(outlier);
var normal = new PointPairList();
normals.Add(normal);
if (ratios.Count > 0)
{
var ratio = protein[0].FindITraqChannelItem(dsName, sample.ChannelRatioName).Ratio;
proteins.Add(new PointPair()
{
Y = Math.Log(ratio)
});
ratios.ForEach(m =>
{
if (m.IsOutlier)
{
outlier.Add(new PointPair()
{
Y = Math.Log(m.Ratio)
});
}
else
{
normal.Add(new PointPair()
{
Y = Math.Log(m.Ratio)
});
}
});
}
else
{
//缺失值用missing表示。
proteins.Add(new PointPair()
{
Y = PointPair.Missing
});
}
}
}
panel.AddPoints(proteins, Color.Red, "Ratio");
AddOrdinalPoints(outliers, panel, Color.Green, "Outlier");
AddOrdinalPoints(normals, panel, Color.Black, "");
panel.XAxis.Type = AxisType.Text;
panel.XAxis.Scale.FontSpec.Angle = 90;
panel.XAxis.Scale.TextLabels = xlabels.ToArray();
panel.YAxis.Title.Text = "log(Ratio)";
ZedGraphicExtension.UpdateGraph(zgcGraph);
}