private void EmptyGraph(SrmDocument document)
{
string[] resultNames = GraphData.GetReplicateLabels(document).ToArray();
XAxis.Scale.TextLabels = resultNames;
var originalTextLabels = new string[XAxis.Scale.TextLabels.Length];
Array.Copy(XAxis.Scale.TextLabels, originalTextLabels, XAxis.Scale.TextLabels.Length);
OriginalXAxisLabels = originalTextLabels;
ScaleAxisLabels();
// Add a missing point for each replicate name.
PointPairList pointPairList = new PointPairList();
for (int i = 0; i < resultNames.Length; i++)
pointPairList.Add(AreaGraphData.AreaPointPairMissing(i));
AxisChange();
}
public override void UpdateGraph(bool checkData)
{
_dotpLabels = new GraphObjList();
SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI;
var results = document.Settings.MeasuredResults;
bool resultsAvailable = results != null;
Clear();
if (!resultsAvailable)
{
Title.Text = Resources.AreaReplicateGraphPane_UpdateGraph_No_results_available;
EmptyGraph(document);
return;
}
var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode;
if (selectedTreeNode == null || document.FindNode(selectedTreeNode.Path) == null)
{
EmptyGraph(document);
return;
}
BarSettings.Type = BarType;
Title.Text = null;
DisplayTypeChrom displayType;
if (Equals(PaneKey, PaneKey.PRECURSORS))
{
displayType = DisplayTypeChrom.precursors;
}
else if (Equals(PaneKey, PaneKey.PRODUCTS))
{
displayType = DisplayTypeChrom.products;
}
else
{
displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
}
DocNode selectedNode = selectedTreeNode.Model;
DocNode parentNode = selectedNode;
IdentityPath identityPath = selectedTreeNode.Path;
bool optimizationPresent = results.Chromatograms.Contains(
chrom => chrom.OptimizationFunction != null);
// If the selected tree node is a transition, then its siblings are displayed.
if (selectedTreeNode is TransitionTreeNode)
{
if (displayType == DisplayTypeChrom.single)
{
BarSettings.Type = BarType.Cluster;
}
else
{
SrmTreeNode parentTreeNode = selectedTreeNode.SrmParent;
parentNode = parentTreeNode.Model;
identityPath = parentTreeNode.Path;
}
}
// If the selected node is a peptide with one child, then show the children,
// unless chromatogram display type is total
else if (selectedTreeNode is PeptideTreeNode)
{
var children = ((PeptideDocNode)selectedNode).TransitionGroups
.Where(PaneKey.IncludesTransitionGroup)
.ToArray();
if (children.Length == 1 && displayType != DisplayTypeChrom.total)
{
selectedNode = parentNode = children[0];
identityPath = new IdentityPath(identityPath, parentNode.Id);
}
else
{
BarSettings.Type = BarType.Cluster;
}
}
else if (!(selectedTreeNode is TransitionGroupTreeNode))
{
Title.Text = Resources.AreaReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_peak_area_graph;
CanShowPeakAreaLegend = false;
CanShowDotProduct = false;
return;
}
var parentGroupNode = parentNode as TransitionGroupDocNode;
// If a precursor is going to be displayed with display type single
if (parentGroupNode != null && displayType == DisplayTypeChrom.single)
{
// If no optimization data, then show all the transitions
if (!optimizationPresent)
{
displayType = DisplayTypeChrom.all;
}
// Otherwise, do not stack the bars
else
{
BarSettings.Type = BarType.Cluster;
}
}
int ratioIndex = AreaGraphData.RATIO_INDEX_NONE;
var standardType = IsotopeLabelType.light;
var areaView = AreaGraphController.AreaView;
if (areaView == AreaNormalizeToView.area_ratio_view)
{
ratioIndex = GraphSummary.RatioIndex;
standardType = document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes[ratioIndex];
}
else if (areaView == AreaNormalizeToView.area_global_standard_view)
{
if (document.Settings.HasGlobalStandardArea)
{
ratioIndex = ChromInfo.RATIO_INDEX_GLOBAL_STANDARDS;
}
else
{
areaView = AreaNormalizeToView.none;
}
}
// Sets normalizeData to optimization, maximum_stack, maximum, total, or none
AreaNormalizeToData normalizeData;
if (optimizationPresent && displayType == DisplayTypeChrom.single &&
areaView == AreaNormalizeToView.area_percent_view)
{
normalizeData = AreaNormalizeToData.optimization;
}
else if (areaView == AreaNormalizeToView.area_maximum_view)
{
normalizeData = BarSettings.Type == BarType.Stack
? AreaNormalizeToData.maximum_stack
: AreaNormalizeToData.maximum;
}
else if (BarSettings.Type == BarType.PercentStack)
{
normalizeData = AreaNormalizeToData.total;
}
else
{
normalizeData = AreaNormalizeToData.none;
}
// Calculate graph data points
// IsExpectedVisible depends on ExpectedVisible
ExpectedVisible = AreaExpectedValue.none;
if (parentGroupNode != null &&
displayType != DisplayTypeChrom.total &&
areaView != AreaNormalizeToView.area_ratio_view &&
!(optimizationPresent && displayType == DisplayTypeChrom.single))
{
var displayTrans = GraphChromatogram.GetDisplayTransitions(parentGroupNode, displayType).ToArray();
bool isShowingMs = displayTrans.Any(nodeTran => nodeTran.IsMs1);
bool isShowingMsMs = displayTrans.Any(nodeTran => !nodeTran.IsMs1);
bool isFullScanMs = document.Settings.TransitionSettings.FullScan.IsEnabledMs && isShowingMs;
if (isFullScanMs)
{
if (!isShowingMsMs && parentGroupNode.HasIsotopeDist)
{
ExpectedVisible = AreaExpectedValue.isotope_dist;
}
}
else
{
if (parentGroupNode.HasLibInfo)
{
ExpectedVisible = AreaExpectedValue.library;
}
}
}
var expectedValue = IsExpectedVisible ? ExpectedVisible : AreaExpectedValue.none;
var replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings);
var graphData = new AreaGraphData(document,
parentNode,
displayType,
replicateGroupOp,
ratioIndex,
normalizeData,
expectedValue,
PaneKey);
var aggregateOp = replicateGroupOp.AggregateOp;
// Avoid stacking CVs
if (aggregateOp.Cv || aggregateOp.CvDecimal)
{
BarSettings.Type = BarType.Cluster;
}
int countNodes = graphData.DocNodes.Count;
if (countNodes == 0)
{
ExpectedVisible = AreaExpectedValue.none;
}
CanShowDotProduct = ExpectedVisible != AreaExpectedValue.none &&
areaView != AreaNormalizeToView.area_percent_view;
CanShowPeakAreaLegend = countNodes != 0;
InitFromData(graphData);
// Add data to the graph
int selectedReplicateIndex = SelectedIndex;
if (IsExpectedVisible)
{
if (GraphSummary.ActiveLibrary)
{
selectedReplicateIndex = 0;
}
}
double maxArea = -double.MaxValue;
double sumArea = 0;
// An array to keep track of height of all bars to determine
// where each dot product annotation (if showing) should be placed
var sumAreas = new double[graphData.ReplicateGroups.Count];
// If only one bar to show, then use cluster instead of stack bar type, since nothing to stack
// Important for mean error bar checking below
if (BarSettings.Type == BarType.Stack && countNodes == 1 && graphData.PointPairLists[0].Count == 1)
{
BarSettings.Type = BarType.Cluster;
}
int colorOffset = 0;
if (parentGroupNode != null)
{
// We want the product ion colors to stay the same whether they are displayed:
// 1. In a single pane with the precursor ions (Transitions -> All)
// 2. In a separate pane of the split graph (Transitions -> All AND Transitions -> Split Graph)
// 3. In a single pane by themselves (Transition -> Products)
// We will use an offset in the colors array for cases 2 and 3 so that we do not reuse the precursor ion colors.
var nodeDisplayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
if (displayType == DisplayTypeChrom.products &&
(nodeDisplayType != DisplayTypeChrom.single ||
(nodeDisplayType == DisplayTypeChrom.single && !optimizationPresent)))
{
colorOffset =
GraphChromatogram.GetDisplayTransitions(parentGroupNode, DisplayTypeChrom.precursors).Count();
}
}
int iColor = 0, iCharge = -1;
int?charge = null;
int countLabelTypes = document.Settings.PeptideSettings.Modifications.CountLabelTypes;
for (int i = 0; i < countNodes; i++)
{
var docNode = graphData.DocNodes[i];
var pointPairLists = graphData.PointPairLists[i];
int numSteps = pointPairLists.Count / 2;
for (int iStep = 0; iStep < pointPairLists.Count; iStep++)
{
int step = iStep - numSteps;
var pointPairList = pointPairLists[iStep];
Color color;
var nodeGroup = docNode as TransitionGroupDocNode;
if (parentNode is PeptideDocNode)
{
int iColorGroup = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge);
color = COLORS_GROUPS[iColorGroup % COLORS_GROUPS.Length];
}
else if (displayType == DisplayTypeChrom.total)
{
color = COLORS_GROUPS[iColor % COLORS_GROUPS.Length];
}
else if (docNode.Equals(selectedNode) && step == 0)
{
color = ChromGraphItem.ColorSelected;
}
else
{
color = COLORS_TRANSITION[(iColor + colorOffset) % COLORS_TRANSITION.Length];
}
iColor++;
// If showing ratios, do not add the standard type to the graph,
// since it will always be empty, but make sure the colors still
// correspond with the other graphs.
if (nodeGroup != null && ratioIndex >= 0)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (ReferenceEquals(labelType, standardType))
{
continue;
}
}
string label = graphData.DocNodeLabels[i];
if (step != 0)
{
label = string.Format(Resources.AreaReplicateGraphPane_UpdateGraph_Step__0_, step);
}
BarItem curveItem;
// Only use a MeanErrorBarItem if bars are not going to be stacked.
// TODO(nicksh): AreaGraphData.NormalizeTo does not know about MeanErrorBarItem
if (BarSettings.Type != BarType.Stack && BarSettings.Type != BarType.PercentStack && normalizeData == AreaNormalizeToData.none)
{
curveItem = new MeanErrorBarItem(label, pointPairList, color, Color.Black);
}
else
{
curveItem = new BarItem(label, pointPairList, color);
}
if (0 <= selectedReplicateIndex && selectedReplicateIndex < pointPairList.Count)
{
PointPair pointPair = pointPairList[selectedReplicateIndex];
if (!pointPair.IsInvalid)
{
sumArea += pointPair.Y;
maxArea = Math.Max(maxArea, pointPair.Y);
}
}
// Add area for this transition to each area entry
AddAreasToSums(pointPairList, sumAreas);
curveItem.Bar.Border.IsVisible = false;
curveItem.Bar.Fill.Brush = new SolidBrush(color);
curveItem.Tag = new IdentityPath(identityPath, docNode.Id);
CurveList.Add(curveItem);
}
}
ParentGroupNode = parentGroupNode;
SumAreas = sumAreas;
// Draw a box around the currently selected replicate
if (ShowSelection && maxArea > -double.MaxValue)
{
double yValue;
switch (BarSettings.Type)
{
case BarType.Stack:
// The Math.Min(sumArea, .999) makes sure that if graph is in normalized view
// height of the selection rectangle does not exceed 1, so that top of the rectangle
// can be viewed when y-axis scale maximum is at 1
yValue = (areaView == AreaNormalizeToView.area_maximum_view ? Math.Min(sumArea, .999) : sumArea);
break;
case BarType.PercentStack:
yValue = 99.99;
break;
default:
// Scale the selection box to fit exactly the bar height
yValue = (areaView == AreaNormalizeToView.area_maximum_view ? Math.Min(maxArea, .999) : maxArea);
break;
}
GraphObjList.Add(new BoxObj(selectedReplicateIndex + .5, yValue, 0.99,
yValue, Color.Black, Color.Empty)
{
IsClippedToChartRect = true,
});
}
// Reset the scale when the parent node changes
bool resetAxes = (_parentNode == null || !ReferenceEquals(_parentNode.Id, parentNode.Id));
_parentNode = parentNode;
UpdateAxes(resetAxes, aggregateOp, normalizeData, areaView, standardType);
}
public override void UpdateGraph(bool checkData)
{
_dotpLabels = new GraphObjList();
SrmDocument document = GraphSummary.DocumentUIContainer.DocumentUI;
var results = document.Settings.MeasuredResults;
bool resultsAvailable = results != null;
Clear();
if (!resultsAvailable)
{
Title.Text = Resources.AreaReplicateGraphPane_UpdateGraph_No_results_available;
EmptyGraph(document);
return;
}
var selectedTreeNode = GraphSummary.StateProvider.SelectedNode as SrmTreeNode;
if (selectedTreeNode == null || document.FindNode(selectedTreeNode.Path) == null)
{
EmptyGraph(document);
return;
}
BarSettings.Type = BarType;
Title.Text = null;
DisplayTypeChrom displayType;
if (Equals(PaneKey, PaneKey.PRECURSORS))
{
displayType = DisplayTypeChrom.precursors;
}
else if (Equals(PaneKey, PaneKey.PRODUCTS))
{
displayType = DisplayTypeChrom.products;
}
else
{
displayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
}
DocNode selectedNode = selectedTreeNode.Model;
DocNode parentNode = selectedNode;
IdentityPath identityPath = selectedTreeNode.Path;
bool optimizationPresent = results.Chromatograms.Contains(
chrom => chrom.OptimizationFunction != null);
// If the selected tree node is a transition, then its siblings are displayed.
if (selectedTreeNode is TransitionTreeNode)
{
if (displayType == DisplayTypeChrom.single)
{
BarSettings.Type = BarType.Cluster;
}
else
{
SrmTreeNode parentTreeNode = selectedTreeNode.SrmParent;
parentNode = parentTreeNode.Model;
identityPath = parentTreeNode.Path;
}
}
// If the selected node is a peptide with one child, then show the children,
// unless chromatogram display type is total
else if (selectedTreeNode is PeptideTreeNode)
{
var children = ((PeptideDocNode) selectedNode).TransitionGroups
.Where(PaneKey.IncludesTransitionGroup)
.ToArray();
if (children.Length == 1 && displayType != DisplayTypeChrom.total)
{
selectedNode = parentNode = children[0];
identityPath = new IdentityPath(identityPath, parentNode.Id);
}
else
{
BarSettings.Type = BarType.Cluster;
}
}
else if (!(selectedTreeNode is TransitionGroupTreeNode))
{
Title.Text = Resources.AreaReplicateGraphPane_UpdateGraph_Select_a_peptide_to_see_the_peak_area_graph;
CanShowPeakAreaLegend = false;
CanShowDotProduct = false;
return;
}
var parentGroupNode = parentNode as TransitionGroupDocNode;
// If a precursor is going to be displayed with display type single
if (parentGroupNode != null && displayType == DisplayTypeChrom.single)
{
// If no optimization data, then show all the transitions
if (!optimizationPresent)
displayType = DisplayTypeChrom.all;
// Otherwise, do not stack the bars
else
BarSettings.Type = BarType.Cluster;
}
int ratioIndex = AreaGraphData.RATIO_INDEX_NONE;
var standardType = IsotopeLabelType.light;
var areaView = AreaGraphController.AreaView;
if (areaView == AreaNormalizeToView.area_ratio_view)
{
ratioIndex = GraphSummary.RatioIndex;
standardType = document.Settings.PeptideSettings.Modifications.RatioInternalStandardTypes[ratioIndex];
}
else if (areaView == AreaNormalizeToView.area_global_standard_view)
{
if (document.Settings.HasGlobalStandardArea)
ratioIndex = ChromInfo.RATIO_INDEX_GLOBAL_STANDARDS;
else
areaView = AreaNormalizeToView.none;
}
// Sets normalizeData to optimization, maximum_stack, maximum, total, or none
AreaNormalizeToData normalizeData;
if (optimizationPresent && displayType == DisplayTypeChrom.single &&
areaView == AreaNormalizeToView.area_percent_view)
{
normalizeData = AreaNormalizeToData.optimization;
}
else if (areaView == AreaNormalizeToView.area_maximum_view)
{
normalizeData = BarSettings.Type == BarType.Stack
? AreaNormalizeToData.maximum_stack
: AreaNormalizeToData.maximum;
}
else if (BarSettings.Type == BarType.PercentStack)
{
normalizeData = AreaNormalizeToData.total;
}
else
{
normalizeData = AreaNormalizeToData.none;
}
// Calculate graph data points
// IsExpectedVisible depends on ExpectedVisible
ExpectedVisible = AreaExpectedValue.none;
if (parentGroupNode != null &&
displayType != DisplayTypeChrom.total &&
areaView != AreaNormalizeToView.area_ratio_view &&
!(optimizationPresent && displayType == DisplayTypeChrom.single))
{
var displayTrans = GraphChromatogram.GetDisplayTransitions(parentGroupNode, displayType).ToArray();
bool isShowingMs = displayTrans.Any(nodeTran => nodeTran.IsMs1);
bool isShowingMsMs = displayTrans.Any(nodeTran => !nodeTran.IsMs1);
bool isFullScanMs = document.Settings.TransitionSettings.FullScan.IsEnabledMs && isShowingMs;
if (isFullScanMs)
{
if (!isShowingMsMs && parentGroupNode.HasIsotopeDist)
ExpectedVisible = AreaExpectedValue.isotope_dist;
}
else
{
if (parentGroupNode.HasLibInfo)
ExpectedVisible = AreaExpectedValue.library;
}
}
var expectedValue = IsExpectedVisible ? ExpectedVisible : AreaExpectedValue.none;
var replicateGroupOp = GraphValues.ReplicateGroupOp.FromCurrentSettings(document.Settings);
var graphData = new AreaGraphData(document,
parentNode,
displayType,
replicateGroupOp,
ratioIndex,
normalizeData,
expectedValue,
PaneKey);
var aggregateOp = replicateGroupOp.AggregateOp;
// Avoid stacking CVs
if (aggregateOp.Cv || aggregateOp.CvDecimal)
BarSettings.Type = BarType.Cluster;
int countNodes = graphData.DocNodes.Count;
if (countNodes == 0)
ExpectedVisible = AreaExpectedValue.none;
CanShowDotProduct = ExpectedVisible != AreaExpectedValue.none &&
areaView != AreaNormalizeToView.area_percent_view;
CanShowPeakAreaLegend = countNodes != 0;
InitFromData(graphData);
// Add data to the graph
int selectedReplicateIndex = SelectedIndex;
if (IsExpectedVisible)
{
if (GraphSummary.ActiveLibrary)
selectedReplicateIndex = 0;
}
double maxArea = -double.MaxValue;
double sumArea = 0;
// An array to keep track of height of all bars to determine
// where each dot product annotation (if showing) should be placed
var sumAreas = new double[graphData.ReplicateGroups.Count];
// If only one bar to show, then use cluster instead of stack bar type, since nothing to stack
// Important for mean error bar checking below
if (BarSettings.Type == BarType.Stack && countNodes == 1 && graphData.PointPairLists[0].Count == 1)
BarSettings.Type = BarType.Cluster;
int colorOffset = 0;
if(parentGroupNode != null)
{
// We want the product ion colors to stay the same whether they are displayed:
// 1. In a single pane with the precursor ions (Transitions -> All)
// 2. In a separate pane of the split graph (Transitions -> All AND Transitions -> Split Graph)
// 3. In a single pane by themselves (Transition -> Products)
// We will use an offset in the colors array for cases 2 and 3 so that we do not reuse the precursor ion colors.
var nodeDisplayType = GraphChromatogram.GetDisplayType(document, selectedTreeNode);
if (displayType == DisplayTypeChrom.products &&
(nodeDisplayType != DisplayTypeChrom.single ||
(nodeDisplayType == DisplayTypeChrom.single && !optimizationPresent)))
{
colorOffset =
GraphChromatogram.GetDisplayTransitions(parentGroupNode, DisplayTypeChrom.precursors).Count();
}
}
int iColor = 0, iCharge = -1;
int? charge = null;
int countLabelTypes = document.Settings.PeptideSettings.Modifications.CountLabelTypes;
for (int i = 0; i < countNodes; i++)
{
var docNode = graphData.DocNodes[i];
var pointPairLists = graphData.PointPairLists[i];
int numSteps = pointPairLists.Count/2;
for (int iStep = 0; iStep < pointPairLists.Count; iStep++)
{
int step = iStep - numSteps;
var pointPairList = pointPairLists[iStep];
Color color;
var nodeGroup = docNode as TransitionGroupDocNode;
if (parentNode is PeptideDocNode)
{
int iColorGroup = GetColorIndex(nodeGroup, countLabelTypes, ref charge, ref iCharge);
color = COLORS_GROUPS[iColorGroup % COLORS_GROUPS.Length];
}
else if (displayType == DisplayTypeChrom.total)
{
color = COLORS_GROUPS[iColor%COLORS_GROUPS.Length];
}
else if (docNode.Equals(selectedNode) && step == 0)
{
color = ChromGraphItem.ColorSelected;
}
else
{
color = COLORS_TRANSITION[(iColor + colorOffset) % COLORS_TRANSITION.Length];
}
iColor++;
// If showing ratios, do not add the standard type to the graph,
// since it will always be empty, but make sure the colors still
// correspond with the other graphs.
if (nodeGroup != null && ratioIndex >= 0)
{
var labelType = nodeGroup.TransitionGroup.LabelType;
if (ReferenceEquals(labelType, standardType))
continue;
}
string label = graphData.DocNodeLabels[i];
if (step != 0)
label = string.Format(Resources.AreaReplicateGraphPane_UpdateGraph_Step__0_, step);
BarItem curveItem;
// Only use a MeanErrorBarItem if bars are not going to be stacked.
// TODO(nicksh): AreaGraphData.NormalizeTo does not know about MeanErrorBarItem
if (BarSettings.Type != BarType.Stack && BarSettings.Type != BarType.PercentStack && normalizeData == AreaNormalizeToData.none)
{
curveItem = new MeanErrorBarItem(label, pointPairList, color, Color.Black);
}
else
{
curveItem = new BarItem(label, pointPairList, color);
}
if (0 <= selectedReplicateIndex && selectedReplicateIndex < pointPairList.Count)
{
PointPair pointPair = pointPairList[selectedReplicateIndex];
if (!pointPair.IsInvalid)
{
sumArea += pointPair.Y;
maxArea = Math.Max(maxArea, pointPair.Y);
}
}
// Add area for this transition to each area entry
AddAreasToSums(pointPairList, sumAreas);
curveItem.Bar.Border.IsVisible = false;
curveItem.Bar.Fill.Brush = new SolidBrush(color);
curveItem.Tag = new IdentityPath(identityPath, docNode.Id);
CurveList.Add(curveItem);
}
}
ParentGroupNode = parentGroupNode;
SumAreas = sumAreas;
// Draw a box around the currently selected replicate
if (ShowSelection && maxArea > -double.MaxValue)
{
double yValue;
switch (BarSettings.Type)
{
case BarType.Stack:
// The Math.Min(sumArea, .999) makes sure that if graph is in normalized view
// height of the selection rectangle does not exceed 1, so that top of the rectangle
// can be viewed when y-axis scale maximum is at 1
yValue = (areaView == AreaNormalizeToView.area_maximum_view ? Math.Min(sumArea, .999) : sumArea);
break;
case BarType.PercentStack:
yValue = 99.99;
break;
default:
// Scale the selection box to fit exactly the bar height
yValue = (areaView == AreaNormalizeToView.area_maximum_view ? Math.Min(maxArea, .999) : maxArea);
break;
}
GraphObjList.Add(new BoxObj(selectedReplicateIndex + .5, yValue, 0.99,
yValue, Color.Black, Color.Empty)
{
IsClippedToChartRect = true,
});
}
// Reset the scale when the parent node changes
bool resetAxes = (_parentNode == null || !ReferenceEquals(_parentNode.Id, parentNode.Id));
_parentNode = parentNode;
UpdateAxes(resetAxes, aggregateOp, normalizeData, areaView, standardType);
}
