public static void MakeGeneLengthDistro()
{
try
{
UpdateLog("Scanning annotation element lengths..", true);
Dictionary <string, List <double> > tdict = Genome.GetAllElementLengths();
UpdateLog("Making Distributions..", true);
MultiHisto mHist = new MultiHisto(tdict, 50, ModelDisplayType.Bar);
PlotModel model = new PlotModel {
Title = "Annotation Element Lengths in Base-Pairs"
};
LinearAxis axX = new LinearAxis(AxisPosition.Bottom, 0, mHist.GetXPercentLimit(0.90), "Length (BP)");
LinearAxis axY = new LinearAxis(AxisPosition.Left, 0, mHist.GetYPercentLimit(0.95), "Density");
model.TitlePadding = 10;
axX.AxisTitleDistance = 10;
axY.AxisTitleDistance = 10;
model.Axes.Add(axX);
model.Axes.Add(axY);
mHist.AddToModel(model);
model.IsLegendVisible = true;
MainWindow.InsertGraph(GraphWindow.Gene, model, mHist);
UpdateLog("Made a length distribution graph in the Gene tab.", true);
ProgramState.MadeGeneGraph = true;
}
catch (Exception e) {
ShowMessageWindow(e.Message, true);
}
}
public static void MakeMethyCovDepthScoreDistro()
{
try
{
UpdateLog("Calculating annotation element read depth-coverage scores..", true);
Dictionary <string, List <double> > tdict = Genome.GetAllElementDepthScores();
UpdateLog("Making Distributions..", true);
MultiHisto mHist = new MultiHisto(tdict, 100, ModelDisplayType.Line);
PlotModel model = new PlotModel {
Title = "Annotation Element per-base read coverage depth"
};
LinearAxis axX = new LinearAxis(AxisPosition.Bottom, 0, mHist.GetXPercentLimit(0.9), "Read depth-coverage of element");
LinearAxis axY = new LinearAxis(AxisPosition.Left, 0, mHist.GetYPercentLimit(1), "Density");
model.TitlePadding = 10;
axX.AxisTitleDistance = 10;
axY.AxisTitleDistance = 10;
model.Axes.Add(axX);
model.Axes.Add(axY);
mHist.AddToModel(model);
model.IsLegendVisible = true;
MainWindow.InsertGraph(GraphWindow.Meth, model, mHist);
UpdateLog("Made a depth-coverage score graph in the SAM-read tab.", true);
ProgramState.MadeMethGraph = true;
}
catch (Exception e) {
ShowMessageWindow(e.Message, true);
}
}
public static void MakeMultiHistoRankGraph(Dictionary <string, List <double> > data, GraphWindow grWind,
string xLab, string yLab, string title, RSplitContainer <double> rsc, bool mergeOld)
{
try
{
UpdateLog("Making Odds ratios..", true);
MultiHisto mHist = new MultiHisto(data, 100, ModelDisplayType.Line);
PlotModel model = new PlotModel {
Title = title
};
LinearAxis axX = new LinearAxis(AxisPosition.Bottom, 0, mHist.GetXPercentLimit(1) + 1, xLab);
LinearAxis axY = new LinearAxis(AxisPosition.Left, 0, mHist.GetYPercentLimit(1), yLab);
model.TitlePadding = 10;
axX.AxisTitleDistance = 10;
axY.AxisTitleDistance = 10;
model.Axes.Add(axX);
model.Axes.Add(axY);
mHist.AddToModel(model);
if (mergeOld && RSPToMergeSeries != null)
{
foreach (Series sr in RSPToMergeSeries)
{
model.Series.Add(sr);
}
}
else
{
if (RSPToMergeSeries != null)
{
RSPToMergeSeries.Clear();
}
}
RSPToMergeSeries.AddRange(mHist.GetNextSeries(title.Split(' ')[0]));
model.IsLegendVisible = true;
MainWindow.InsertGraph(grWind, model, mHist);
MainWindow.SetRSplitDoubleContainer(rsc);
UpdateLog("Made a density-based Rank/Split graph...", true);
ProgramState.MadeGlobalGraph = true;
}
catch (Exception e) {
ShowMessageWindow(e.Message, true);
}
}
public static void MakeGeneBaseRatio()
{
try
{
UpdateLog("Scanning base ratios for each included genomic annotation/element..", true);
Dictionary <string, List <double> > tdict = Genome.FindAllElementBaseRatios();
UpdateLog("Making Distributions..", true);
MultiHisto mHist = new MultiHisto(tdict, 50, ModelDisplayType.Line);
PlotModel model = new PlotModel {
Title = "Annotation Element Base Ratios: CG / (CG + AT)"
};
LinearAxis axX = new LinearAxis(AxisPosition.Bottom, 0, 1, "Ratio");
LinearAxis axY = new LinearAxis(AxisPosition.Left, 0, mHist.GetYPercentLimit(1), "Density");
//LogarithmicAxis
model.TitlePadding = 10;
axX.AxisTitleDistance = 10;
axY.AxisTitleDistance = 10;
model.Axes.Add(axX);
model.Axes.Add(axY);
mHist.AddToModel(model);
model.IsLegendVisible = true;
model.LegendItemSpacing = 10;
MainWindow.InsertGraph(GraphWindow.Gene, model, mHist);
UpdateLog("Made a base ratio graph in the Gene tab,", true);
ProgramState.MadeGeneGraph = true;
} catch (Exception e) {
ShowMessageWindow(e.Message, true);
}
}
