public static void MakeGenomeBaseRatio()
{
try
{
UpdateLog("Fragmenting " + Genome.ShortFileName + " Into 200bp Fragments & calculcating base ratios..", true);
List <double> ratios = Genome.FindAllBaseRatios();
int bcount = Math.Min(ratios.Count / 300, 40);
DoublesHisto dHisto = new DoublesHisto(ratios, bcount, "CG Ratio", false, ModelDisplayType.Bar);
PlotModel model = new PlotModel {
Title = "For 200bp fragments: Base Ratio: CG / (AT + CG)"
};
LinearAxis axX = new LinearAxis(AxisPosition.Bottom, 0, 1, "CG Ratio");
LinearAxis axY = new LinearAxis(AxisPosition.Left, 0, dHisto.GetYPercentLimit(1), "Density");
model.TitlePadding = 10;
axX.AxisTitleDistance = 10;
axY.AxisTitleDistance = 10;
model.Axes.Add(axX);
model.Axes.Add(axY);
dHisto.AddToModel(model);
model.IsLegendVisible = true;
MainWindow.InsertGraph(GraphWindow.Genome, model, dHisto);
UpdateLog("Made a base ratio graph in the Genome tab.", true);
ProgramState.MadeGenomeGraph = true;
}
catch (Exception e) {
ShowMessageWindow(e.Message, true);
}
}
public MultiHisto(Dictionary <string, List <double> > dict, int buckets, ModelDisplayType dtype) : base()
{
histos = new List <GraphingClass> ();
double fullMax = 0;
double fullMin = 999999999;
double stdMin = 999999999;
double stdMax = 0;
foreach (KeyValuePair <string, List <double> > kvp in dict)
{
if (kvp.Value.Count > 5)
{
DoublesHisto h = new DoublesHisto(kvp.Value, buckets, kvp.Key, true, dtype);
histos.Add(h);
fullMax = Math.Max(h.GetLocalMax(), fullMax);
fullMin = Math.Min(h.GetLocalMin(), fullMin);
stdMax = Math.Max(h.GetPlusTwoStdDevs(), stdMax);
stdMin = Math.Min(h.GetMinusTwoStdDevs(), stdMin);
}
}
stdMin = Math.Max(0, stdMin);
List <double> increments = DoublesHisto.CreateBoundaryIncrements(fullMin, fullMax, stdMin, stdMax, buckets);
int pos = 1;
int cnt = histos.Count;
foreach (DoublesHisto h in histos)
{
h.SetBoundaryIncrements(increments);
h.CountToBins(fullMin);
h.SetTotalHistos(cnt, pos);
pos++;
}
}