private ToolStripMenuItem MakeToolStripMenuItem(GroupComparisonDef groupComparisonDef)
{
return(new ToolStripMenuItem(groupComparisonDef.Name, null, (sender, args) =>
{
SkylineWindow.ShowGroupComparisonWindow(groupComparisonDef.Name);
}));
}
private void VerifyFoldChanges(SrmDocument testDocument, GroupComparisonDef groupComparisonDef,
IDictionary <string, LinearFitResult> expectedResults)
{
var groupComparer = new GroupComparer(groupComparisonDef, testDocument, new QrFactorizationCache());
foreach (var protein in testDocument.MoleculeGroups)
{
var groupComparisonResult = groupComparer.CalculateFoldChanges(protein, null).FirstOrDefault();
LinearFitResult expectedResult;
if (expectedResults.TryGetValue(protein.Name, out expectedResult))
{
Assert.IsNotNull(groupComparisonResult);
var foldChange = groupComparisonResult.LinearFitResult;
Assert.AreEqual(expectedResult.EstimatedValue, foldChange.EstimatedValue, 1E-5);
Assert.AreEqual(expectedResult.DegreesOfFreedom, foldChange.DegreesOfFreedom);
Assert.AreEqual(expectedResult.StandardError, foldChange.StandardError, 1E-5);
Assert.AreEqual(expectedResult.TValue, foldChange.TValue, 1E-5);
Assert.AreEqual(expectedResult.PValue, foldChange.PValue, 1E-5);
}
else
{
Assert.IsNull(groupComparisonResult);
var standardPeptides = protein.Molecules.Where(mol => !string.IsNullOrEmpty(mol.GlobalStandardType)).ToArray();
Assert.AreNotEqual(0, standardPeptides.Length);
}
}
}
public void ChangeGroupComparison(Control owner, string name, Action <EditGroupComparisonDlg> action)
{
GroupComparisonDef def = null;
RunDlg <EditGroupComparisonDlg>(() => def = Settings.Default.GroupComparisonDefList.EditItem(owner,
FindGroupComparison(name),
Settings.Default.GroupComparisonDefList, SkylineWindow), d =>
{
action(d);
d.OkDialog();
});
RunUI(() =>
{
int index = Settings.Default.GroupComparisonDefList.ToList().FindIndex(g => g.Name == name);
if (index >= 0)
{
Settings.Default.GroupComparisonDefList[index] = def;
SkylineWindow.ModifyDocument(Resources.SkylineWindow_AddGroupComparison_Add_Fold_Change,
doc => doc.ChangeSettings(
doc.Settings.ChangeDataSettings(
doc.Settings.DataSettings.AddGroupComparisonDef(
def))));
}
});
}
protected void comboControlValue_SelectedIndexChanged(object sender, EventArgs e)
{
if (_inChangeSettings)
{
return;
}
GroupComparisonDef = GroupComparisonDef.ChangeControlValue(comboControlValue.SelectedItem as string);
}
protected void cbxTreatMissingAsZero_CheckedChanged(object sender, EventArgs e)
{
if (_inChangeSettings)
{
return;
}
GroupComparisonDef = GroupComparisonDef.ChangeUseZeroForMissingPeaks(((CheckBox)sender).Checked);
}
private void radioScope_CheckedChanged(object sender, EventArgs e)
{
if (_inChangeSettings)
{
return;
}
GroupComparisonDef = GroupComparisonDef.ChangePerProtein(radioScopeProtein.Checked);
}
private void comboSummaryMethod_SelectedIndexChanged(object sender, EventArgs e)
{
if (_inChangeSettings)
{
return;
}
GroupComparisonDef = GroupComparisonDef.ChangeSummarizationMethod(
comboSummaryMethod.SelectedItem as SummarizationMethod ?? SummarizationMethod.DEFAULT);
}
protected void comboControlAnnotation_SelectedIndexChanged(object sender, EventArgs e)
{
if (_inChangeSettings)
{
return;
}
var comboControlAnnotation = (ComboBox)sender;
GroupComparisonDef =
GroupComparisonDef.ChangeControlAnnotation(
comboControlAnnotation.SelectedItem as string);
}
protected void comboNormalizationMethod_SelectedIndexChanged(object sender, EventArgs e)
{
if (_inChangeSettings)
{
return;
}
var normalizationMethod = comboNormalizationMethod.SelectedItem as NormalizationMethod ??
NormalizationMethod.NONE;
GroupComparisonDef = GroupComparisonDef
.ChangeNormalizationMethod(normalizationMethod);
}
public GroupComparisonDef FindGroupComparison(string name)
{
GroupComparisonDef def = null;
RunUI(() =>
{
def = SkylineWindow.DocumentUI.Settings.DataSettings.GroupComparisonDefs.FirstOrDefault(g =>
g.Name == name);
});
return(def);
}
public EditGroupComparisonDlg(IDocumentUIContainer documentContainer,
GroupComparisonDef groupComparisonDef, IEnumerable <GroupComparisonDef> existingGroupComparisons)
: this(new GroupComparisonModel(documentContainer, null) { GroupComparisonDef = groupComparisonDef })
{
_originalGroupComparisonDef = groupComparisonDef;
_existingGroupComparisons = existingGroupComparisons;
if (documentContainer == null)
{
btnPreview.Visible = false;
}
_pushChangesToDocument = false;
tbxName.Text = groupComparisonDef.Name ?? string.Empty;
}
protected void comboCaseValue_SelectedIndexChanged(object sender, EventArgs e)
{
if (_inChangeSettings)
{
return;
}
string caseValue = comboCaseValue.SelectedItem as string;
if (string.IsNullOrEmpty(caseValue))
{
caseValue = null;
}
GroupComparisonDef = GroupComparisonDef.ChangeCaseValue(caseValue);
}
public void TestFoldChangeWithNoNormalization()
{
SrmDocument testDocument = OpenTestDocument();
var expectedResults = MsStatsTestUtil.ReadExpectedResults(typeof(MsStatsNormalizationTest),
"BrudererSubsetNoNormalization_TestingResult.csv");
GroupComparisonDef groupComparisonDef = new GroupComparisonDef("test")
.ChangeControlValue("S2")
.ChangeCaseValue("S1")
.ChangeControlAnnotation("Condition")
.ChangeIdentityAnnotation("BioReplicate")
.ChangePerProtein(true)
.ChangeNormalizationMethod(NormalizationMethod.NONE);
VerifyFoldChanges(testDocument, groupComparisonDef, expectedResults);
}
public DataSettings AddGroupComparisonDef(GroupComparisonDef groupComparisonDef)
{
var groupComparisonDefs = GroupComparisonDefs.ToList();
int index = GroupComparisonDefs.IndexOf(def => def.Name == groupComparisonDef.Name);
if (index < 0)
{
groupComparisonDefs.Add(groupComparisonDef);
}
else
{
groupComparisonDefs[index] = groupComparisonDef;
}
return(ChangeGroupComparisonDefs(groupComparisonDefs));
}
protected void tbxConfidenceLevel_TextChanged(object sender, EventArgs e)
{
if (_inChangeSettings)
{
return;
}
double confidenceLevel;
MessageBoxHelper helper = new MessageBoxHelper(this, false);
if (!helper.ValidateDecimalTextBox(tbxConfidenceLevel, 0, 100, out confidenceLevel))
{
return;
}
GroupComparisonDef = GroupComparisonDef.ChangeConfidenceLevelTimes100(confidenceLevel);
}
public static ViewSpec GetDefaultViewSpec(GroupComparisonDef groupComparisonDef,
IList <FoldChangeBindingSource.FoldChangeRow> foldChangeRows)
{
bool showPeptide;
bool showLabelType;
bool showMsLevel;
if (foldChangeRows.Any())
{
showPeptide = foldChangeRows.Any(row => null != row.Peptide);
showLabelType = foldChangeRows.Select(row => row.IsotopeLabelType).Distinct().Count() > 1;
showMsLevel = foldChangeRows.Select(row => row.MsLevel).Distinct().Count() > 1;
}
else
{
showPeptide = !groupComparisonDef.PerProtein;
showLabelType = false;
showMsLevel = false;
}
// ReSharper disable NonLocalizedString
var columns = new List <PropertyPath>
{
PropertyPath.Root.Property("Protein")
};
if (showPeptide)
{
columns.Add(PropertyPath.Root.Property("Peptide"));
}
if (showMsLevel)
{
columns.Add(PropertyPath.Root.Property("MsLevel"));
}
if (showLabelType)
{
columns.Add(PropertyPath.Root.Property("IsotopeLabelType"));
}
columns.Add(PropertyPath.Root.Property("FoldChangeResult"));
columns.Add(PropertyPath.Root.Property("FoldChangeResult").Property("AdjustedPValue"));
// ReSharper restore NonLocalizedString
var viewSpec = new ViewSpec()
.SetName(DefaultViewName)
.SetRowType(typeof(FoldChangeBindingSource.FoldChangeRow))
.SetColumns(columns.Select(col => new ColumnSpec(col)));
return(viewSpec);
}
public void RunTestFoldChangeEqualizeMedians(bool asSmallMolecules)
{
SrmDocument testDocument = OpenTestDocument();
if (testDocument == null)
{
Assume.IsTrue(asSmallMolecules);
return;
}
var expectedResults = MsStatsTestUtil.ReadExpectedResults(typeof(MsStatsNormalizationTest),
"BrudererSubsetEqualizeMedians_TestingResult.csv");
GroupComparisonDef groupComparisonDef = new GroupComparisonDef("test")
.ChangeControlValue("S2")
.ChangeCaseValue("S1")
.ChangeControlAnnotation("Condition")
.ChangeIdentityAnnotation("BioReplicate")
.ChangePerProtein(true)
.ChangeNormalizationMethod(NormalizationMethod.EQUALIZE_MEDIANS);
VerifyFoldChanges(testDocument, groupComparisonDef, expectedResults);
}
protected void comboIdentityAnnotation_SelectedIndexChanged(object sender, EventArgs e)
{
if (_inChangeSettings)
{
return;
}
string identityAnnotation = comboIdentityAnnotation.SelectedItem as string;
if (string.IsNullOrEmpty(identityAnnotation))
{
GroupComparisonDef = GroupComparisonDef
.ChangeIdentityAnnotation(null)
.ChangeAverageTechnicalReplicates(false);
}
else
{
GroupComparisonDef = GroupComparisonDef
.ChangeIdentityAnnotation(identityAnnotation)
.ChangeAverageTechnicalReplicates(true);
}
}
private void tbxQValueCutoff_TextChanged(object sender, EventArgs e)
{
if (_inChangeSettings)
{
return;
}
if (string.IsNullOrEmpty(tbxQValueCutoff.Text.Trim()))
{
GroupComparisonDef = GroupComparisonDef.ChangeQValueCutoff(null);
}
else
{
MessageBoxHelper helper = new MessageBoxHelper(this, false);
double qValueCutoff;
if (!helper.ValidateDecimalTextBox(tbxQValueCutoff, 0, 1, out qValueCutoff))
{
return;
}
GroupComparisonDef = GroupComparisonDef.ChangeQValueCutoff(qValueCutoff);
}
}
public EditGroupComparisonDlg(IDocumentContainer documentContainer,
GroupComparisonDef groupComparisonDef, IEnumerable <GroupComparisonDef> existingGroupComparisons)
: base(new GroupComparisonModel(documentContainer, null) { GroupComparisonDef = groupComparisonDef })
{
InitializeComponent();
Icon = Resources.Skyline;
_originalGroupComparisonDef = groupComparisonDef;
_existingGroupComparisons = existingGroupComparisons;
if (documentContainer == null)
{
btnPreview.Visible = false;
}
tbxName.Text = groupComparisonDef.Name ?? string.Empty;
tbxConfidenceLevel.TextChanged += tbxConfidenceLevel_TextChanged;
comboControlAnnotation.SelectedIndexChanged += comboControlAnnotation_SelectedIndexChanged;
comboCaseValue.SelectedIndexChanged += comboCaseValue_SelectedIndexChanged;
comboControlValue.SelectedIndexChanged += comboControlValue_SelectedIndexChanged;
comboIdentityAnnotation.SelectedIndexChanged += comboIdentityAnnotation_SelectedIndexChanged;
comboNormalizationMethod.SelectedIndexChanged += comboNormalizationMethod_SelectedIndexChanged;
radioScopeProtein.CheckedChanged += radioScope_CheckedChanged;
radioScopePeptide.CheckedChanged += radioScope_CheckedChanged;
}
private bool RequiresAdvanced(GroupComparisonDef groupComparisonDef)
{
return(groupComparisonDef.QValueCutoff.HasValue ||
groupComparisonDef.SummarizationMethod != SummarizationMethod.AVERAGING ||
groupComparisonDef.UseZeroForMissingPeaks);
}
public void ShowFormattingDialog()
{
var foldChangeRows = _bindingListSource.OfType <RowItem>()
.Select(rowItem => rowItem.Value)
.OfType <FoldChangeBindingSource.FoldChangeRow>()
.ToArray();
var backup = GroupComparisonDef.ColorRows.Select(r => (MatchRgbHexColor)r.Clone()).ToArray();
// This list will later be used as a BindingList, so we have to create a mutable clone
var copy = GroupComparisonDef.ColorRows.Select(r => (MatchRgbHexColor)r.Clone()).ToList();
using (var form = new VolcanoPlotFormattingDlg(this, copy, foldChangeRows,
rows =>
{
EditGroupComparisonDlg.ChangeGroupComparisonDef(false, GroupComparisonModel, GroupComparisonDef.ChangeColorRows(rows));
UpdateGraph();
}))
{
if (form.ShowDialog() == DialogResult.OK)
{
EditGroupComparisonDlg.ChangeGroupComparisonDef(true, GroupComparisonModel, GroupComparisonDef);
}
else
{
EditGroupComparisonDlg.ChangeGroupComparisonDef(false, GroupComparisonModel, GroupComparisonDef.ChangeColorRows(backup));
}
UpdateGraph();
}
}
public static void ChangeGroupComparisonDef(bool pushChangesToDocument, GroupComparisonModel model, GroupComparisonDef groupDef)
{
if (pushChangesToDocument)
{
Program.MainWindow.ModifyDocument(
GroupComparisonStrings.GroupComparisonSettingsForm_GroupComparisonDef_Change_Group_Comparison,
doc => model.ApplyChangesToDocument(doc, groupDef),
AuditLogEntry.SettingsLogFunction
);
Settings.Default.GroupComparisonDefList.Add(groupDef);
}
else
{
model.GroupComparisonDef = groupDef;
}
}