Line chart trendline options for provided parameters to CalculateCurveFit API #7192

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Merged

cnathe merged 14 commits into develop from fb_trendlineProvidedParams

Nov 20, 2025

api/src/org/labkey/api/data/JsonWriter.java

-Original file line number
+Diff line change
@@ Expand Up @@
             props.put("wrappedColumnName", cinfo == null ? null : cinfo.getWrappedColumnName());
             props.put("valueExpression", cinfo == null ? null : cinfo.getValueExpression());
+            props.put("displayWidth", cinfo == null ? null : cinfo.getDisplayWidth());
             ColumnInfo displayField = dc.getDisplayColumnInfo();
             if (displayField != null && displayField != cinfo)
@@ Expand Down @@

api/src/org/labkey/api/data/statistics/StatsService.java

-Original file line number
+Diff line change
@@ Expand Up / @@ -18,8 +18,10 @@ @@
     import org.jetbrains.annotations.Nullable;
     import org.labkey.api.services.ServiceRegistry;
+    import java.util.ArrayList;
     import java.util.Arrays;
     import java.util.Collection;
+    import java.util.List;
     /**
      * Created by klum on 1/14/14.
@@ Expand All / @@ -38,22 +40,27 @@ static void setInstance(StatsService impl) @@
         enum CurveFitType
         {
-            THREE_PARAMETER("Three Parameter", "3pl"),
-            FOUR_PARAMETER("Four Parameter", "4pl"),
-            FIVE_PARAMETER("Five Parameter", "5pl"),
-            THREE_PARAMETER_ALT("3 Parameter", "3param"),
-            FOUR_PARAMETER_SIMPLEX("4 Parameter", "4param"),
-            POLYNOMIAL("Polynomial", "poly"),
-            LINEAR("Linear", "linear"),
-            NONE("None", "none");
+            // TODO see updated labels for these equations in genericChartHelper.js TRENDLINE_OPTIONS
+            // we should update the labels here as well at some point (but this would like need to include an upgrade script for saved chart configs)
+            THREE_PARAMETER("Three Parameter", "3pl", Arrays.asList("min", "max", "inflection")),
+            FOUR_PARAMETER("Four Parameter", "4pl", Arrays.asList("min", "max", "slope", "inflection")),
+            FIVE_PARAMETER("Five Parameter", "5pl", Arrays.asList("min", "max", "slope", "inflection", "asymmetry")),
+            THREE_PARAMETER_ALT("3 Parameter", "3param", Arrays.asList("min", "max", "inflection")),
+            FOUR_PARAMETER_SIMPLEX("4 Parameter", "4param", Arrays.asList("min", "max", "slope", "inflection")),
+            FIVE_PARAMETER_ALT("5 Parameter", "5param", Arrays.asList("min", "max", "slope", "inflection", "asymmetry")),
+            POLYNOMIAL("Polynomial", "poly", Arrays.asList("coefficients")),
+            LINEAR("Linear", "linear", Arrays.asList("slope", "intercept")),
+            NONE("None", "none", Arrays.asList());
             private final String _label;
             private final String _colSuffix;
+            private final List<String> _parameterNames = new ArrayList<>();
-            CurveFitType(String label, String colSuffix)
+            CurveFitType(String label, String colSuffix, List<String> parameterNames)
             {
                 _label = label;
                 _colSuffix = colSuffix;
+                _parameterNames.addAll(parameterNames);
             }
             // Consider : moving the col suffix portion of this back into assays...
@@ Expand All / @@ -68,6 +75,11 @@ public String getLabel() @@
                 return _label;
             }
+            public List<String> getParameterNames()
+            {
+                return _parameterNames;
+            }
             @Override
             public String toString()
             {
@@ Expand Down @@

core/src/org/labkey/core/statistics/FiveParameterCurveFit.java

-Original file line number
+Diff line change
@@ -0,0 +1,41 @@
+    package org.labkey.core.statistics;
+    import org.jetbrains.annotations.Nullable;
+    import org.labkey.api.data.statistics.DoublePoint;
+    import static org.labkey.api.data.statistics.StatsService.CurveFitType.FIVE_PARAMETER_ALT;
+    /*
+    * Equation: Asymmetrical Sigmoidal, 5PL (aka Richards five-parameter dose-response curve)
+    * Y = Bottom + (Numerator/Denominator)
+    * Numerator = Top - Bottom
+    * Denominator = (1+(2^(1/S)-1)*((EC50/X)^HillSlope))^S
+    */
+    public class FiveParameterCurveFit extends ParameterCurveFit
+    {
+        public FiveParameterCurveFit(DoublePoint[] data, @Nullable Double asymptoteMin, @Nullable Double asymptoteMax)
+        {
+            super(data, FIVE_PARAMETER_ALT, asymptoteMin, asymptoteMax);
+        }
+        @Override
+        public double solveForX(double y)
+        {
+            throw new UnsupportedOperationException("Not implemented");
+        }
+        @Override
+        public double fitCurve(double x, SigmoidalParameters params)
+        {
+            if (params != null)
+            {
+                double topMinusBottom = params.getMax() - params.getMin();
+                double exponent = 1.0 / params.getAsymmetry();
+                double base = Math.pow(2.0, exponent) - 1.0;
+                double ec50OverXPowerHillSlope = Math.pow(params.getInflection() / x, params.getSlope());
+                double denominator = Math.pow(1.0 + (base * ec50OverXPowerHillSlope), params.getAsymmetry());
+                return params.getMin() + (topMinusBottom / denominator);
+            }
+            throw new IllegalArgumentException("No curve fit parameters for " + _fitType.name());
+        }
+    }

core/src/org/labkey/core/statistics/ParameterCurveFit.java

-Original file line number
+Diff line change
@@ Expand Up @@
             {
                 case THREE_PARAMETER, THREE_PARAMETER_ALT -> adjustedRSquared(parameters, 3);
                 case FOUR_PARAMETER -> adjustedRSquared(parameters, 4);
-                case FIVE_PARAMETER -> adjustedRSquared(parameters, 5);
+                case FIVE_PARAMETER, FIVE_PARAMETER_ALT -> adjustedRSquared(parameters, 5);
                 default -> throw new IllegalStateException("Unsupported curve fit type: " + _fitType.name());
             };
         }
@@ Expand Down Expand Up @@
                             switch (_fitType)
                             {
                                 case FIVE_PARAMETER:
+                                case FIVE_PARAMETER_ALT:
                                     for (double asymmetryFactor = 0; asymmetryFactor < Math.PI; asymmetryFactor += Math.PI / 30)
                                     {
                                         parameters.asymmetry = asymmetryFactor;
@@ Expand Down @@

core/src/org/labkey/core/statistics/StatsServiceImpl.java

            
                      Original file line number
                      Diff line number
                      Diff line change
                  
    @@ -71,6 +71,8 @@ public CurveFit getCurveFit(CurveFitType type, DoublePoint[] data, @Nullable Dou
  
                    return new ThreeParameterCurveFit(data, asymptoteMax);

                case FOUR_PARAMETER_SIMPLEX:

                    return new FourParameterSimplex(data);

                case FIVE_PARAMETER_ALT:

                    return new FiveParameterCurveFit(data, asymptoteMin, asymptoteMax);

                case THREE_PARAMETER:

                    return new ParameterCurveFit(data, type, 0.0, asymptoteMax);

                case FOUR_PARAMETER:

    @@ -133,6 +135,7 @@ public void TestCurveFits() throws Exception
  
                v1.setResults(CurveFitType.THREE_PARAMETER, new CurveResults(3.09, .065, .065));

                v1.setResults(CurveFitType.THREE_PARAMETER_ALT, new CurveResults(3.09, .065, .065));

                v1.setResults(CurveFitType.FOUR_PARAMETER, new CurveResults(2.5, .031, .045));

                v1.setResults(CurveFitType.FIVE_PARAMETER_ALT, new CurveResults(2.08, .046, .054));

                v1.setResults(CurveFitType.FIVE_PARAMETER, new CurveResults(2.2, .046, .054));

                v1.setResults(CurveFitType.LINEAR, new CurveResults(6.8, .070, .070));

                validations.add(v1);

    @@ -143,6 +146,7 @@ public void TestCurveFits() throws Exception
  
                v2.setResults(CurveFitType.THREE_PARAMETER, new CurveResults(2.93, .414, .414));

                v2.setResults(CurveFitType.THREE_PARAMETER_ALT, new CurveResults(2.93, .414, .414));

                v2.setResults(CurveFitType.FOUR_PARAMETER, new CurveResults(3.4, .403, .403));

                v2.setResults(CurveFitType.FIVE_PARAMETER_ALT, new CurveResults(2.44, .420, .420));

                v2.setResults(CurveFitType.FIVE_PARAMETER, new CurveResults(3.1, .420, .420));

                v2.setResults(CurveFitType.LINEAR, new CurveResults(36.8, .553, .553));

                validations.add(v2);

    @@ -153,6 +157,7 @@ public void TestCurveFits() throws Exception
  
                v3.setResults(CurveFitType.THREE_PARAMETER, new CurveResults(5.0, .078, .078));

                v3.setResults(CurveFitType.THREE_PARAMETER_ALT, new CurveResults(5.0, .078, .078));

                v3.setResults(CurveFitType.FOUR_PARAMETER, new CurveResults(4.7, .048, .049));

                v3.setResults(CurveFitType.FIVE_PARAMETER_ALT, new CurveResults(4.6, .049, .051));

                v3.setResults(CurveFitType.FIVE_PARAMETER, new CurveResults(4.6, .080, .082));

                v3.setResults(CurveFitType.LINEAR, new CurveResults(5.9, .070, .070));

                validations.add(v3);

    @@ -163,6 +168,7 @@ public void TestCurveFits() throws Exception
  
                v4.setResults(CurveFitType.THREE_PARAMETER, new CurveResults(4.05, .265, .265));

                v4.setResults(CurveFitType.THREE_PARAMETER_ALT, new CurveResults(4.05, .265, .265));

                v4.setResults(CurveFitType.FOUR_PARAMETER, new CurveResults(4.5, .226, .247));

                v4.setResults(CurveFitType.FIVE_PARAMETER_ALT, new CurveResults(3.29, .245, .251));

                v4.setResults(CurveFitType.FIVE_PARAMETER, new CurveResults(3.7, .245, .262));

                v4.setResults(CurveFitType.LINEAR, new CurveResults(27.5, .374, .374));

                validations.add(v4);

    @@ -173,6 +179,7 @@ public void TestCurveFits() throws Exception
  
                v5.setResults(CurveFitType.THREE_PARAMETER, new CurveResults(7.86, .281, .281));

                v5.setResults(CurveFitType.THREE_PARAMETER_ALT, new CurveResults(7.86, .281, .281));

                v5.setResults(CurveFitType.FOUR_PARAMETER, new CurveResults(5, .201, .263));

                v5.setResults(CurveFitType.FIVE_PARAMETER_ALT, new CurveResults(4.105, .221, .277));

                v5.setResults(CurveFitType.FIVE_PARAMETER, new CurveResults(5.1, .221, .277));

                v5.setResults(CurveFitType.LINEAR, new CurveResults(38.0, .363, .363));

                validations.add(v5);

    @@ -187,9 +194,9 @@ public void TestCurveFits() throws Exception
  
                            CurveResults results = validation.getResults(fitType);

                            // validate calculated and expected fit error and auc

                            assertEquals(results.getFitError(), fit.getFitError(), 0.05);

                            assertEquals(results.getAuc(), fit.calculateAUC(AUCType.NORMAL), 0.005);

                            assertEquals(results.getPositiveAuc(), fit.calculateAUC(AUCType.POSITIVE), 0.005);

                            assertEquals(fitType.getLabel(), results.getFitError(), fit.getFitError(), 0.05);

                            assertEquals(fitType.getLabel(), results.getAuc(), fit.calculateAUC(AUCType.NORMAL), 0.005);

                            assertEquals(fitType.getLabel(), results.getPositiveAuc(), fit.calculateAUC(AUCType.POSITIVE), 0.005);

                        }

                    }

                }

    @@ -328,6 +335,15 @@ public void TestCurveFitParameters() throws Exception
  
                fit.setLogXScale(true);

                verifySigmoidalParameters(fit, 0.67, 4.0, 2.246, 0.095, 1.466);

                assertEquals(0.997, fit.rSquared(fit.getParameters()), delta);

                fit = service.getCurveFit(CurveFitType.FIVE_PARAMETER_ALT, data1);

                fit.setLogXScale(false);

                verifySigmoidalParameters(fit, 0.67, 3.17, 9.5144, 0.096, 0.2094);

                assertEquals(0.9978, fit.rSquared(fit.getParameters()), delta);

                fit = service.getCurveFit(CurveFitType.FIVE_PARAMETER_ALT, data1, null, 4.0);

                fit.setLogXScale(true);

                verifySigmoidalParameters(fit, 0.67, 4.0, 1.7321, 0.0946, 3.0369);

                assertEquals(0.9207, fit.rSquared(fit.getParameters()), delta);

            }

            @Test

    @@ -353,6 +369,12 @@ public void TestCurveFitParametersNAbCase() throws Exception
  
                assertEquals(3.493, fit.getFitError(), delta);

                assertEquals(0.990, fit.rSquared(fit.getParameters()), delta);

                fit = service.getCurveFit(CurveFitType.FIVE_PARAMETER_ALT, data1);

                fit.setLogXScale(true);

                verifySigmoidalParameters(fit, -2.0, 93.0, -1.1106, 10.6605, 0.2094);

                assertEquals(2.3816, fit.getFitError(), delta);

                assertEquals(0.9954, fit.rSquared(fit.getParameters()), delta);

                fit = service.getCurveFit(CurveFitType.FOUR_PARAMETER, data1);

                fit.setLogXScale(true);

                verifySigmoidalParameters(fit, -2.0, 103.0, -0.325, 6.907, 1.0);

core/src/org/labkey/core/statistics/ThreeParameterCurveFit.java

-Original file line number
+Diff line change
@@ Expand Up / @@ -43,10 +43,4 @@ public double fitCurve(double x, SigmoidalParameters params) @@
             }
             throw new IllegalArgumentException("No curve fit parameters for " + _fitType.name());
         }
-        @Override
-        public double adjustedRSquared(SigmoidalParameters parameters)
-        {
-            return adjustedRSquared(parameters, 3);
-        }
     }

visualization/resources/web/vis/chartWizard/chartTypeDialog/trendlineField.js

-Original file line number
+Diff line change
@@ Expand Up / @@ -8,7 +8,7 @@ Ext4.define('LABKEY.vis.TrendlineField', { @@
         baseQueryKey: null,
         initData: null,
-        options: ['', 'Linear', 'Polynomial', '3 Parameter', 'Three Parameter', '4 Parameter', 'Four Parameter', 'Five Parameter'],
+        options: ['', 'Linear', 'Polynomial', '3 Parameter', 'Three Parameter', '4 Parameter', 'Four Parameter', 'Five Parameter', '5 Parameter'],
         initComponent: function() {
             if (this.initData == null)
@@ Expand Down @@

visualization/resources/web/vis/chartWizard/genericChartPanel.js

-Original file line number
+Diff line change
@@ Expand Up / @@ -1023,6 +1023,7 @@ Ext4.define('LABKEY.ext4.GenericChartPanel', { @@
                 config.geomOptions.trendlineType = this.trendline.trendlineType;
                 config.geomOptions.trendlineAsymptoteMin = this.trendline.trendlineAsymptoteMin;
                 config.geomOptions.trendlineAsymptoteMax = this.trendline.trendlineAsymptoteMax;
+                config.geomOptions.trendlineParameters = this.trendline.trendlineParameters;
             }
             if (this.getCustomChartOptions)
@@ Expand Down Expand Up / @@ -1325,6 +1326,7 @@ Ext4.define('LABKEY.ext4.GenericChartPanel', { @@
                         trendlineType: chartConfig.geomOptions.trendlineType,
                         trendlineAsymptoteMin: chartConfig.geomOptions.trendlineAsymptoteMin,
                         trendlineAsymptoteMax: chartConfig.geomOptions.trendlineAsymptoteMax,
+                        trendlineParameters: chartConfig.geomOptions.trendlineParameters,
                     }
                 }
             }
@@ Expand Down @@

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Line chart trendline options for provided parameters to CalculateCurveFit API #7192

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