private static RegressionLine GetRegression(TargetMap <double> knownIrts, DbIrtPeptide[] matchingPeptides, int?minPoints, out RegressionGraphData graphData)
{
graphData = null;
var matchingPeptideIrts = new TargetMap <List <double> >(matchingPeptides.Select(pep =>
new KeyValuePair <Target, List <double> >(pep.ModifiedTarget, new List <double>())));
foreach (var pep in matchingPeptides)
{
var list = matchingPeptideIrts[pep.ModifiedTarget];
list.Add(pep.Irt);
}
var listX = new List <double>();
var listY = new List <double>();
var targets = new Dictionary <int, Target>();
foreach (var(i, kvp) in matchingPeptideIrts.Where(kvp => kvp.Value.Count > 0).Select((kvp, i) => Tuple.Create(i, kvp)))
{
targets[i] = kvp.Key;
listX.Add(new Statistics(kvp.Value).Median());
listY.Add(knownIrts[kvp.Key]);
}
var regressionMinPoints = minPoints ?? RCalcIrt.MinStandardCount(knownIrts.Count);
var removed = new List <Tuple <double, double> >();
if (!IrtRegression.TryGet <RegressionLine>(listX, listY, regressionMinPoints, out var regression, removed))
{
return(null);
}
var outliers = new HashSet <int>();
for (var i = 0; i < listX.Count; i++)
{
if (removed.Contains(Tuple.Create(listX[i], listY[i])))
{
outliers.Add(i);
}
}
graphData = new RegressionGraphData
{
Title = Resources.ChooseIrtStandardPeptidesDlg_OkDialog_Linear_regression,
LabelX = Resources.ChooseIrtStandardPeptidesDlg_OkDialog_Library_iRTs,
LabelY = Resources.ChooseIrtStandardPeptidesDlg_OkDialog_Known_iRTs,
XValues = listX.ToArray(),
YValues = listY.ToArray(),
Tooltips = targets.ToDictionary(target => target.Key, target => target.Value.ToString()),
OutlierIndices = outliers,
RegressionLine = regression,
MinCorrelation = RCalcIrt.MIN_IRT_TO_TIME_CORRELATION,
MinPoints = regressionMinPoints,
};
return(regression as RegressionLine);
}
private double GetR(IIrtRegression regression, bool includeOutliers)
{
var r = IrtRegression.R(regression);
if (!double.IsNaN(r))
{
return(r);
}
var pointSet = !includeOutliers?RegularPoints.ToArray() : RegularPoints.Concat(OutlierPoints).ToArray();
var statsX = new Statistics(pointSet.Select(point => point.X));
var statsY = new Statistics(pointSet.Select(point => point.Y));
return(statsY.R(statsX));
}
public AddIrtPeptidesDlg(
AddIrtPeptidesLocation location,
ProcessedIrtAverages processed,
IReadOnlyCollection <Target> existingPeptides,
IReadOnlyCollection <Target> overwritePeptides,
IReadOnlyCollection <Target> keepPeptides)
{
InitializeComponent();
Icon = Resources.Skyline;
_regressionGraphData = new Dictionary <DataGridViewRow, RegressionGraphData[]>();
var successStyle = new DataGridViewCellStyle {
BackColor = Color.LightGreen
};
var failStyle = new DataGridViewCellStyle {
BackColor = Color.LightCoral
};
foreach (var data in processed.ProviderData)
{
var missingIndices = new HashSet <int>();
var outlierIndices = new HashSet <int>();
for (var i = 0; i < data.Peptides.Count; i++)
{
if (data.Peptides[i].Missing)
{
missingIndices.Add(i);
}
else if (data.Peptides[i].Outlier)
{
outlierIndices.Add(i);
}
}
string regressionName;
if (data.RegressionSuccess)
{
regressionName = data.Regression == null
? Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_Regression
: Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_Regression_Refined;
}
else
{
regressionName = Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_Regression_Attempted;
}
var graphData = new RegressionGraphData
{
Title = data.RetentionTimeProvider.Name,
LabelX = Resources.AddIrtsResultsDlg_dataGridView_CellContentClick_Measured,
LabelY = Resources.AddIrtPeptidesDlg_dataGridView_CellContentClick_iRT,
XValues = data.Peptides.Select(peptide => peptide.RetentionTime.GetValueOrDefault()).ToArray(),
YValues = data.Peptides.Select(peptide => peptide.Irt).ToArray(),
Tooltips = Enumerable.Range(0, data.Peptides.Count).ToDictionary(i => i, i => data.Peptides[i].Target.ToString()),
MissingIndices = missingIndices,
OutlierIndices = outlierIndices,
RegressionLine = data.RegressionRefined,
RegressionLineCurrent = data.Regression,
RegressionName = regressionName,
ShowCurrentCorrelation = true,
MinCorrelation = RCalcIrt.MIN_IRT_TO_TIME_CORRELATION,
MinPoints = data.MinPoints
};
string filename;
try
{
filename = Path.GetFileName(data.RetentionTimeProvider.Name);
}
catch (Exception)
{
filename = data.RetentionTimeProvider.Name;
}
dataGridView.Rows.Add(
filename,
graphData.RegularPoints.Count,
data.RegressionRefined != null ? data.RegressionRefined.DisplayEquation : string.Empty,
data.RegressionRefined != null ? IrtRegression.R(data.RegressionRefined).ToString(@"F03") : IrtRegression.R(data.Regression).ToString(@"F03"),
data.RegressionSuccess ? Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_Success : Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_Failed);
var lastRow = dataGridView.Rows[dataGridView.RowCount - 1];
lastRow.DefaultCellStyle = data.RegressionSuccess ? successStyle : failStyle;
lastRow.Tag = data;
_regressionGraphData[lastRow] = new[] { graphData };
}
PeptidesCount = processed.DbIrtPeptides.Count() - existingPeptides.Count - overwritePeptides.Count - keepPeptides.Count;
RunsConvertedCount = processed.ProviderData.Count(data => data.RegressionSuccess);
RunsFailedCount = processed.ProviderData.Count - RunsConvertedCount;
string locationStr;
switch (location)
{
default:
locationStr = Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_iRT_database;
break;
case AddIrtPeptidesLocation.spectral_library:
locationStr = Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_spectral_library;
break;
}
if (PeptidesCount == 0)
{
labelPeptidesAdded.Text = string.Format(Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_No_new_peptides_will_be_added_to_the__0__, locationStr);
}
else if (PeptidesCount == 1)
{
labelPeptidesAdded.Text = string.Format(Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_1_new_peptide_will_be_added_to_the__0__, locationStr);
}
else
{
labelPeptidesAdded.Text = string.Format(labelPeptidesAdded.Text, PeptidesCount, locationStr);
}
if (RunsConvertedCount == 0)
{
labelRunsConverted.Visible = false;
}
else
{
labelRunsConverted.Text = RunsConvertedCount > 1
? string.Format(labelRunsConverted.Text, RunsConvertedCount)
: Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_1_run_was_successfully_converted;
}
if (RunsFailedCount == 0)
{
labelRunsFailed.Visible = false;
}
else
{
labelRunsFailed.Text = RunsFailedCount > 1
? string.Format(labelRunsFailed.Text, RunsFailedCount)
: Resources.AddIrtPeptidesDlg_AddIrtPeptidesDlg_1_run_was_not_converted_due_to_insufficient_correlation;
}
listExisting.Items.AddRange(existingPeptides.Cast <object>().ToArray());
listOverwrite.Items.AddRange(overwritePeptides.Cast <object>().ToArray());
listKeep.Items.AddRange(keepPeptides.Cast <object>().ToArray());
labelExisting.Text = string.Format(labelExisting.Text, listExisting.Items.Count);
labelOverwrite.Text = string.Format(labelOverwrite.Text, listOverwrite.Items.Count);
labelKeep.Text = string.Format(labelKeep.Text, listKeep.Items.Count);
panelExisting.Anchor &= ~AnchorStyles.Bottom;
if (!processed.ProviderData.Any())
{
dataGridView.Visible = false;
panelOverwrite.Top -= dataGridView.Height;
panelKeep.Top -= dataGridView.Height;
panelExisting.Top -= dataGridView.Height;
Height -= dataGridView.Height;
}
if (listOverwrite.Items.Count == 0)
{
panelOverwrite.Visible = false;
panelKeep.Top -= panelOverwrite.Height;
panelExisting.Top -= panelOverwrite.Height;
Height -= panelOverwrite.Height;
}
if (listKeep.Items.Count == 0)
{
panelKeep.Visible = false;
panelExisting.Top -= panelKeep.Height;
Height -= panelKeep.Height;
}
panelExisting.Anchor |= AnchorStyles.Bottom;
if (listExisting.Items.Count == 0)
{
panelExisting.Visible = false;
Height -= panelExisting.Height;
}
if (!listOverwrite.Items.OfType <object>().Any() && !listKeep.Items.OfType <object>().Any() && !listExisting.Items.OfType <object>().Any())
{
if (processed.ProviderData.Any())
{
dataGridView.Anchor |= AnchorStyles.Bottom;
}
else
{
FormBorderStyle = FormBorderStyle.FixedDialog;
}
}
}
