/// <summary>
/// Plot mean quality scores at the sequence-level
/// </summary>
/// <param name="filename">Filename of the output image file</param>
/// <param name="height">Height of the plot in pixels</param>
/// <param name="width">Width of the plot in pixels</param>
public void PlotQualityScoreBySequence(string filename, int height = ShoHelper.HeightDefault, int width = ShoHelper.WidthDefault)
{
if (!this.Analyzer.HasRunContentBySequence)
{
throw new ArgumentException("Unable to plot. Need to process quality score data first.");
}
var bins = ShoHelper.CreateBins((int)this.Analyzer.BaseQualityScoreMin, (int)this.Analyzer.BaseQualityScoreMax, 2);
var hist = new Histogram(this.Analyzer.QualityScoreBySequenceMeans, bins);
ShoChart f = ShoHelper.CreateBasicShoChart(
false,
height,
width,
"Number of reads",
"Mean quality score (" + this.Analyzer.FormatType.ToString() + ")",
"Mean quality score by sequence " + titleBanner
);
// set y-axis labels
//f.SetYLabels(ShoHelper.GetIntegerAxisLabels(0, this.Analyzer.Count), null);
f.Bar(bins, hist.Count);
f.SaveImage(filename);
}
/// <summary>
/// Generate a histogram of GC content over all sequences.
/// </summary>
/// <param name="filename">Filename of the output image file</param>
/// <param name="height">Height of the plot in pixels</param>
/// <param name="width">Width of the plot in pixels</param>
public void PlotGCContentBySequence(string filename, int height = ShoHelper.HeightDefault, int width = ShoHelper.WidthDefault)
{
if (this.Analyzer.GCContentBySequenceArray == null)
{
throw new ArgumentNullException("this.analyzer.SymbolCountByPositionTable");
}
int binSize = 5;
var bins = ShoHelper.CreateBins(0, 100, binSize);
var hist = new Histogram(this.Analyzer.GCContentBySequenceArray, bins);
ShoChart f = ShoHelper.CreateBasicShoChart(
false,
height,
width,
"Number of reads",
"GC content (%; bin size = " + binSize + ")",
"GC content by sequence " + titleBanner
);
var xLabelPositions = ShoHelper.CreateBins(1, 21);
f.SetXLabels(xLabelPositions, bins);
f.Bar(bins, hist.Count);
//f.DundasChart.Series[0].ChartType = SeriesChartType.Spline;
f.SaveImage(filename);
}
/// <summary>
/// Plot the distribution of sequence lengths
/// </summary>
/// <param name="filename">Filename of the output image file</param>
/// <param name="height">Height of the plot in pixels</param>
/// <param name="width">Width of the plot in pixels</param>
public void PlotSequenceLengthDistribution(string filename, int height = ShoHelper.HeightDefault, int width = ShoHelper.WidthDefault)
{
var hist = new Histogram(this.Analyzer.ReadLengths);
ShoChart f = ShoHelper.CreateBasicShoChart(
false,
height,
width,
"Number of reads",
"Length (bp)",
"Sequence length distribution " + titleBanner
);
f.HorizontalMinorGridlinesVisible = true;
//f.SetYLabels(ShoHelper.CreateBins(0, (int)this.Analyzer.Count), null);
f.Bar(hist.BinCenter, hist.Count);
f.SaveImage(filename);
}
