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); } }