void UpdateGroupedGraphWithGrowthData()
{
this.Cursor = Cursors.WaitCursor;
try
{
GraphPane Graph = plotGroupModeling.GraphPane;
Graph.CurveList.Clear();
Graph.Title.Text = "Growth Plots";
Graph.XAxis.Title.Text = "Hours";
if (chkTreatShowLog.Checked)
{
Graph.YAxis.Title.Text = "Log [OD600]";
}
else
{
Graph.YAxis.Title.Text = "OD600";
}
Graph.Legend.Position = LegendPos.InsideTopLeft;
Graph.Legend.FontSpec.Size = 8f;
Graph.Legend.IsHStack = true;
SymbolType SymboltoUse = SymbolType.Circle;
Dictionary <string, GrowthCurve> curData = GetDictionaryOfGrowthRateData();
for (int i = 1; i < SelectablePlateMap.MAX_GROUP_ASSIGNMENTS; i++)
{
Color groupColor;
var curNames = selectPlatesForGroupModel.GetNamesOfWellsAssignedToGroup(i, out groupColor);
string GroupName = "";
if (TreatmentTextBoxes[i] != null)
{
GroupName = TreatmentTextBoxes[i].Text;
}
if (GroupName == "")
{
GroupName = "Treatment: " + i.ToString();
}
foreach (string name in curNames)
{
if (curData.ContainsKey(name))
{
GrowthCurve GD = curData[name];
PointPairList XY;
if (chkTreatShowLog.Checked)
{
XY = new PointPairList(GD.TimeValues_As_Double, GD.LogODValues);
}
else
{
XY = new PointPairList(GD.TimeValues_As_Double, GD.ODValues);
}
Graph.AddCurve(GroupName, XY, groupColor, SymboltoUse);
}
}
}
if (chkTreatLegend.Checked)
{
Graph.Legend.IsVisible = true;
}
else
{
Graph.Legend.IsVisible = false;
}
Graph.XAxis.Scale.MaxGrace = .05;
plotGroupModeling.AxisChange();
plotGroupModeling.Invalidate();
this.Cursor = Cursors.Default;
}
catch (Exception thrown)
{ MessageBox.Show("Could not make graph, talk to nigel.\n\nError is:\n" + thrown.Message, "Graph Error", MessageBoxButtons.OK, MessageBoxIcon.Error); }
finally { this.Cursor = Cursors.Default; }
}
private void RemakeTreatmentGraphWith2(Get2ValuesForTreatment FunctionForData, String Title)
{
this.Cursor = Cursors.WaitCursor;
try
{
GraphPane Graph = plotTreatments.GraphPane;
Graph.CurveList.Clear();
Graph.Title.Text = Title;
Graph.XAxis.Title.Text = "Treatments";
Graph.YAxis.Title.Text = "";
Graph.Legend.Position = LegendPos.InsideTopLeft;
Graph.Legend.FontSpec.Size = 8f;
Graph.Legend.IsHStack = true;
SymbolType SymboltoUse = SymbolType.Circle;
Dictionary <string, GrowthCurve> curData = GetDictionaryOfGrowthRateData();
for (int i = 1; i < SelectablePlateMap.MAX_GROUP_ASSIGNMENTS; i++)
{
Color groupColor;
List <double> xVals = new List <double>();
var curNames = selectablePlateMap1.GetNamesOfWellsAssignedToGroup(i, out groupColor);
string GroupName = "";
if (TreatmentTextBoxes[i] != null)
{
GroupName = TreatmentTextBoxes[i].Text;
}
if (GroupName == "")
{
GroupName = "Treatment: " + i.ToString();
}
PointPairList XY = new PointPairList();
foreach (string name in curNames)
{
if (curData.ContainsKey(name))
{
GrowthCurve GD = curData[name];
PointPair xy = SafeGet(FunctionForData, GD);
if (xy != null)
{
XY.Add(xy);
}
}
}
if (XY.Count > 0)
{
LineItem li = Graph.AddCurve(GroupName, XY, groupColor, SymboltoUse);
li.Line.IsVisible = false;
li.Symbol.Fill = new Fill(groupColor);
}
}
if (chkTreatLegend.Checked)
{
Graph.Legend.IsVisible = true;
}
else
{
Graph.Legend.IsVisible = false;
}
Graph.XAxis.Scale.MaxGrace = .05;
plotTreatments.AxisChange();
plotTreatments.Invalidate();
this.Cursor = Cursors.Default;
}
catch (Exception thrown)
{ MessageBox.Show("Could not make graph, talk to nigel.\n\nError is:\n" + thrown.Message, "Graph Error", MessageBoxButtons.OK, MessageBoxIcon.Error); }
finally { this.Cursor = Cursors.Default; }
}
void UpdateTreatmentGraphWithQQPlot(bool useLinear = false)
{
this.Cursor = Cursors.WaitCursor;
try
{
List <double> residuals = new List <double>();
Dictionary <string, GrowthCurve> curData = GetDictionaryOfGrowthRateData();
for (int i = 1; i < SelectablePlateMap.MAX_GROUP_ASSIGNMENTS; i++)
{
Color groupColor;
var curNames = selectablePlateMap1.GetNamesOfWellsAssignedToGroup(i, out groupColor);
foreach (string name in curNames)
{
if (curData.ContainsKey(name))
{
GrowthCurve GD = curData[name];
if (!useLinear)
{
residuals.AddRange(GD.FittedResidualValues.Select(x => x.y));
}
else
{
residuals.AddRange(GD.LinFit.Residuals);
}
}
}
}
var res = residuals;
res.Sort();
var res2 = DoubleArray.From(res);
res2 = res2 - res2.Mean();
res2 = res2.Divide(res2.Std());
double temp = 1.0 / Convert.ToDouble(res.Count);
DoubleArray d = new DoubleArray(res.Count);
d[0] = 1 - Math.Pow(0.5, temp);
d[res.Count - 1] = Math.Pow(0.5, temp);
int n = res.Count;
for (int i = 0; i < (res.Count - 1); i++)
{
d[i] = ((i + 1) - .3175) / (n + .365);
}
//DoubleArray ll = DoubleArray.From(d);
ShoNS.MathFunc.ArrayMathInPlace.CdfNormInv(d);
//now to graph
GraphPane Graph = plotTreatments.GraphPane;
Graph.CurveList.Clear();
Graph.Title.Text = "QQ Plot of Residuals";
Graph.XAxis.Title.Text = "Theoretical Quantiles";
Graph.YAxis.Title.Text = "Sample Quantiles";
Graph.Legend.FontSpec.Size = 10f;
Graph.Legend.IsHStack = true;
SymbolType SymboltoUse = SymbolType.Circle;
Graph.Legend.IsVisible = false;
PointPairList XY = new PointPairList(d.ToArray(), res2.ToArray());
var b = Graph.AddCurve("Points", XY, Color.Green, SymboltoUse);
b.Line.IsVisible = false;
double minm = d.Min();
double maxm = d.Max();
XY = new PointPairList(new double[] { minm, maxm }, new double[] { minm, maxm });
Graph.AddCurve("1 to 1", XY, Color.Blue, SymbolType.None);
Graph.XAxis.Scale.MaxGrace = .05;
plotTreatments.AxisChange();
plotTreatments.Invalidate();
this.Cursor = Cursors.Default;
}
catch (Exception thrown)
{ MessageBox.Show("Could not make graph, talk to nigel.\n\nError is:\n" + thrown.Message, "Graph Error", MessageBoxButtons.OK, MessageBoxIcon.Error); }
finally { this.Cursor = Cursors.Default; }
}
void UpdateTreatmentGraphWithResidualData(bool OnlyShowFitted = false, bool ShowLinearResiduals = false, bool showQuadResiduals = false)
{
this.Cursor = Cursors.WaitCursor;
try
{
GraphPane Graph = plotTreatments.GraphPane;
Graph.CurveList.Clear();
Graph.Title.Text = "Growth Plots";
Graph.XAxis.Title.Text = "Hours";
Graph.YAxis.Title.Text = "Residuals";
Graph.Legend.Position = LegendPos.InsideTopLeft;
Graph.Legend.FontSpec.Size = 8f;
Graph.Legend.IsHStack = true;
SymbolType SymboltoUse = SymbolType.Circle;
Dictionary <string, GrowthCurve> curData = GetDictionaryOfGrowthRateData();
for (int i = 1; i < SelectablePlateMap.MAX_GROUP_ASSIGNMENTS; i++)
{
Color groupColor;
var curNames = selectablePlateMap1.GetNamesOfWellsAssignedToGroup(i, out groupColor);
string GroupName = "";
if (TreatmentTextBoxes[i] != null)
{
GroupName = TreatmentTextBoxes[i].Text;
}
if (GroupName == "")
{
GroupName = "Treatment: " + i.ToString();
}
foreach (string name in curNames)
{
if (curData.ContainsKey(name))
{
GrowthCurve GD = curData[name];
PointPairList XY;
List <double> Xs;
List <double> Ys;
if (ShowLinearResiduals)
{
Xs = new List <double>();
Ys = new List <double>();
if (GD.LinFit != null)
{
Xs.AddRange(GD.LinFit.X);
Ys.AddRange(GD.LinFit.ReturnResidualsAfterExpTransform());
}
}
else if (showQuadResiduals)
{
Xs = new List <double>();
Ys = new List <double>();
if (GD.QuadModel != null && GD.QuadModel.SuccessfulFit)
{
Xs.AddRange(GD.QuadModel.X);
Ys.AddRange(GD.QuadModel.ReturnResidualsAfterExpTransform);
}
}
else
{
GD.GetResiduals(OnlyShowFitted, out Xs, out Ys);
XY = new PointPairList(Xs.ToArray(), Ys.ToArray());
//GD.LinFit.GetResiduals(out Xs, out Ys);
}
XY = new PointPairList(Xs.ToArray(), Ys.ToArray());
Graph.AddCurve(GroupName, XY, groupColor, SymboltoUse);
}
}
}
if (chkTreatLegend.Checked)
{
Graph.Legend.IsVisible = true;
}
else
{
Graph.Legend.IsVisible = false;
}
Graph.XAxis.Scale.MaxGrace = .05;
plotTreatments.AxisChange();
plotTreatments.Invalidate();
this.Cursor = Cursors.Default;
}
catch (Exception thrown)
{ MessageBox.Show("Could not make graph, talk to nigel.\n\nError is:\n" + thrown.Message, "Graph Error", MessageBoxButtons.OK, MessageBoxIcon.Error); }
finally { this.Cursor = Cursors.Default; }
}
void UpdateTreatmentGraphWithSlopeData(bool LogScale = false)
{
this.Cursor = Cursors.WaitCursor;
try
{
GraphPane Graph = plotTreatments.GraphPane;
Graph.CurveList.Clear();
Graph.Title.Text = "Doubling Times From Neighboring Point Interpolation ";
Graph.YAxis.Title.Text = "Doubling Time";
Graph.Legend.Position = LegendPos.InsideTopLeft;
Graph.Legend.FontSpec.Size = 8f;
Graph.Legend.IsHStack = true;
//SymbolType SymboltoUse = SymbolType.Circle;
Dictionary <string, GrowthCurve> curData = GetDictionaryOfGrowthRateData();
for (int i = 1; i < SelectablePlateMap.MAX_GROUP_ASSIGNMENTS; i++)
{
Color groupColor;
var curNames = selectablePlateMap1.GetNamesOfWellsAssignedToGroup(i, out groupColor);
string GroupName = "";
if (TreatmentTextBoxes[i] != null)
{
GroupName = TreatmentTextBoxes[i].Text;
}
if (GroupName == "")
{
GroupName = "Treatment: " + i.ToString();
}
foreach (string name in curNames)
{
if (curData.ContainsKey(name))
{
GrowthCurve GD = curData[name];
HashSet <double> ht = new HashSet <double>(GD.TimeValues_As_Double);
PointPairList XYFit = new PointPairList();
PointPairList ZWFit = new PointPairList();
if (!LogScale)
{
GD.SlopeValues.Where(x => ht.Contains(x.x)).ToList().ForEach(x => XYFit.Add(x.x, x.y));
GD.SlopeValues.Where(x => !ht.Contains(x.x)).ToList().ForEach(x => XYFit.Add(x.x, x.y));
}
else
{
GD.SlopeValues.Where(x => ht.Contains(x.x)).ToList().ForEach(x => XYFit.Add(Math.Log10(x.x), x.y));
GD.SlopeValues.Where(x => !ht.Contains(x.x)).ToList().ForEach(x => XYFit.Add(Math.Log10(x.x), x.y));
}
Graph.AddCurve(GroupName, XYFit, groupColor, SymbolType.Circle);
Graph.AddCurve(GroupName, ZWFit, groupColor, SymbolType.Star);
}
}
}
if (!LogScale)
{
Graph.XAxis.Title.Text = "OD Reading at Center Point";
}
else
{
Graph.XAxis.Title.Text = "Log OD Reading at Center Point";
}
if (chkTreatLegend.Checked)
{
Graph.Legend.IsVisible = true;
}
else
{
Graph.Legend.IsVisible = false;
}
Graph.XAxis.Scale.MaxGrace = .05;
plotTreatments.AxisChange();
plotTreatments.Invalidate();
this.Cursor = Cursors.Default;
}
catch (Exception thrown)
{ MessageBox.Show("Could not make graph, talk to nigel.\n\nError is:\n" + thrown.Message, "Graph Error", MessageBoxButtons.OK, MessageBoxIcon.Error); }
finally { this.Cursor = Cursors.Default; }
}
private void UpdateTreatmentGraphsWithDifference(string BaseLineWell = "C4")
{
try
{
var q = GetDictionaryOfGrowthRateData();
double[] Baseline = q["C4"].ODValues;
GraphPane Graph = plotTreatments.GraphPane;
Graph.CurveList.Clear();
Graph.Title.Text = "Growth Plots";
Graph.XAxis.Title.Text = "Hours";
Graph.YAxis.Title.Text = "OD Reading-" + BaseLineWell;
Graph.Legend.Position = LegendPos.InsideTopLeft;
Graph.Legend.FontSpec.Size = 8f;
Graph.Legend.IsHStack = true;
SymbolType SymboltoUse = SymbolType.Circle;
Dictionary <string, GrowthCurve> curData = GetDictionaryOfGrowthRateData();
for (int i = 1; i < SelectablePlateMap.MAX_GROUP_ASSIGNMENTS; i++)
{
Color groupColor;
var curNames = selectablePlateMap1.GetNamesOfWellsAssignedToGroup(i, out groupColor);
string GroupName = "";
if (TreatmentTextBoxes[i] != null)
{
GroupName = TreatmentTextBoxes[i].Text;
}
if (GroupName == "")
{
GroupName = "Treatment: " + i.ToString();
}
foreach (string name in curNames)
{
if (curData.ContainsKey(name))
{
GrowthCurve GD = curData[name];
PointPairList XY;
double[] difs = Baseline.Zip(GD.ODValues, (x, y) => x - y).ToArray();
XY = new PointPairList(GD.TimeValues_As_Double, difs);
Graph.AddCurve(GroupName, XY, groupColor, SymboltoUse);
}
}
}
if (chkTreatLegend.Checked)
{
Graph.Legend.IsVisible = true;
}
else
{
Graph.Legend.IsVisible = false;
}
Graph.XAxis.Scale.MaxGrace = .05;
plotTreatments.AxisChange();
plotTreatments.Invalidate();
this.Cursor = Cursors.Default;
}
catch (Exception thrown)
{
MessageBox.Show("Could not make graph, talk to nigel.\n\nError is:\n" + thrown.Message, "Graph Error", MessageBoxButtons.OK, MessageBoxIcon.Error);
}
finally { this.Cursor = Cursors.Default; }
}
private void OnEnable()
{
_target = (GrowthCurve)target;
}
public abstract void DoSensitivityAnalysis(GrowthCurve GD, ArrayPlot AP);
