private void makeSlidingWindowOccurencePlot()
{
MitoPaintedAssembler.RaiseStatusEvent("\tStarting sliding window plot");
var list = GetAverageInSlidingCoverageWindows().ToList();
double[] xvals = list.Select(x => (double)x.Key).ToArray();
double[] yvals = list.Select(x => x.Value).ToArray();
var scutoff = PoissonCoverageCutoffCount.ToString();
string line = "lines(c(0,16569),c(" + scutoff + "," + scutoff + "),col=\"red\",lwd=3)";
rInt.PlotPDF(xvals, yvals, OutputFilePrefix + "Windowed" + this.ScanningWindowSize.ToString() + ".pdf", "Windowed occurence", "Insert Size", "Window Average", new List <string>()
{
line
});
MitoPaintedAssembler.RaiseStatusEvent("\tFinished sliding window plot");
}
/// <summary>
/// Plot the intervals and densities as we move along.
/// </summary>
private void makeTotalCoveragePlotOverSearchRange()
{
var counts = GetRangeToEvaluate();
var engine = rInt.CurrentEngine;
lock (engine)
{
var yvals = engine.CreateNumericVector(counts);
var xvals = engine.CreateNumericVector(Enumerable.Range(LowEndOfSearchRange.Value, counts.Count).Select(x => (double)x));
string fname = OutputFilePrefix + "SearchRange.pdf";
var scutoff = PoissonCoverageCutoffCount.ToString();
string line = "lines(c(0,16569),c(" + scutoff + "," + scutoff + "),col=\"red\",lwd=3)";
rInt.PlotPDF(xvals, yvals, fname, "Template Length Distribution", "Length", "Counts", new List <string>()
{
line
});
}
}
private void makeTotalCoveragePlot()
{
var lowVal = LowEndOfSearchRange.Value;
var highVal = HighEndOfSearchRange.Value;
var y_high = (countsOfSize.Max() * 5).ToString();
var engine = rInt.CurrentEngine;
lock (engine)
{
var xvals = engine.CreateNumericVector(Enumerable.Range(1, countsOfSize.Length).Select(x => (double)x));
var yvals = engine.CreateNumericVector(countsOfSize);
string fname = OutputFilePrefix + "FullRange.pdf";
var scutoff = PoissonCoverageCutoffCount.ToString();
List <string> addCmds = new List <string> (3);
string line = "lines(c(0,16569),c(" + scutoff + "," + scutoff + "),col=\"red\",lwd=3)";
addCmds.Add(line);
line = "lines(rep(" + lowVal.ToString() + ",2),c(0, " + y_high + "),col=\"red\",lwd=3)";
addCmds.Add(line);
line = "lines(rep(" + highVal.ToString() + ",2),c(0, " + y_high + "),col=\"red\",lwd=3)";
addCmds.Add(line);
rInt.PlotPDF(xvals, yvals, fname, "Template Length Distribution", "Template Length", "Counts of Reads", addCmds);
}
}
