Read count model simulation and viewer for lphy #56

popsizefunc-lphy-studio/build.gradle.kts → phylonco-lphy-studio/build.gradle.kts

@@ -10,7 +10,7 @@ plugins {
 version = "0.0.1-SNAPSHOT"//-SNAPSHOT"
 
 dependencies {
-    implementation(project(":popsizefunc-lphy"))
+    implementation(project(":phylonco-lphy"))
 
     api("io.github.linguaphylo:lphy-studio:1.5.1-SNAPSHOT") //-SNAPSHOT
 
@@ -51,7 +51,7 @@ tasks.jar {
         // shared attr in the root build
         attributes(
             "Main-Class" to maincls,
-            "Implementation-Title" to "Pop-size function",
+            "Implementation-Title" to "Phylonco Lphy Studio",
             "Implementation-Vendor" to developers,
         )
     }
@@ -63,7 +63,7 @@ publishing {
         create<MavenPublication>(project.name) {
             artifactId = project.base.archivesName.get()
             pom {
-                description.set("The LPhy extension including pop-size functions.")
+                description.set("The LPhy Studio extension.")
                 developers {
                     developer {
                         name.set(developers)

popsizefunc-lphy-studio/src/main/java/module-info.java → phylonco-lphy-studio/src/main/java/module-info.java

@@ -1,12 +1,14 @@
+import readcountmodel.lphystudio.viewer.ReadCountModelViewer;
+
 module popsizefunc.lphy.studio {
 
-    requires transitive popsizefunc.lphy;
     requires transitive lphystudio;
+    requires phylonco.lphy;
 
     // Viewer SPI
     uses lphystudio.app.graphicalmodelpanel.viewer.Viewer;
     // declare what service interface the provider intends to use
-    provides lphystudio.app.graphicalmodelpanel.viewer.Viewer with popsizefunc.lphystudio.viewer.PopSizeFuncViewer;
+    provides lphystudio.app.graphicalmodelpanel.viewer.Viewer with ReadCountModelViewer;
 
     // Note: to adapt with the system not using Java module but using class path,
     // they need to be declared inside META-INF/services/lphystudio.app.graphicalmodelpanel.viewer.Viewer as well.

phylonco-lphy-studio/src/main/java/readcountmodel/lphystudio/viewer/ReadCountModelComponent.java

@@ -0,0 +1,9 @@
+package readcountmodel.lphystudio.viewer;
+
+import javax.swing.*;
+
+public class ReadCountModelComponent extends JComponent {
+
+    //TODO check AlignmentComponent
+
+}

phylonco-lphy-studio/src/main/java/readcountmodel/lphystudio/viewer/ReadCountModelViewer.java

@@ -0,0 +1,33 @@
+package readcountmodel.lphystudio.viewer;
+
+import lphy.base.evolution.coalescent.PopulationFunction;
+import lphy.core.model.Value;
+import lphystudio.app.graphicalmodelpanel.viewer.Viewer;
+import phylonco.lphy.evolution.readcountmodel.ReadCountData;
+import phylonco.lphy.evolution.readcountmodel.ReadCountModel;
+
+import javax.swing.*;
+
+public class ReadCountModelViewer implements Viewer{
+    public ReadCountModelViewer(){}
+
+    @Override
+    public boolean match(Object value) {
+        return value instanceof ReadCountData ||
+                (value instanceof Value && ((Value) value).value() instanceof ReadCountData);
+
+    }
+
+    @Override
+    public JComponent getViewer(Object value) {
+        if (match(value)) {
+            return new JTextArea(value.toString());
+        }
+        String text = ((Value<ReadCountData>) value).value().toString();
+        return new JTextArea(text);
+    }
+
+    @Override
+    public String toString() { return "Read Count Viewer"; }
+}
+

popsizefunc-lphy-studio/src/main/resources/services/lphy.core.spi.Extension → phylonco-lphy-studio/src/main/resources/services/lphy.core.spi.Extension

@@ -3,4 +3,5 @@
 # META-INF/services must be under src for Intellij
 # Class requires a public no-args constructor
 
-popsizefunc.lphystudio.spi.PopSizeFuncViewerImpl
+# popsizefunc.lphystudio.spi.PopSizeFuncViewerImpl
+readcountmodel.lphystudio.viewer.ReadCountModelViewer

popsizefunc-lphy-studio/src/main/resources/services/lphystudio.app.graphicalmodelpanel.viewer.Viewer → phylonco-lphy-studio/src/main/resources/services/lphystudio.app.graphicalmodelpanel.viewer.Viewer

@@ -7,4 +7,5 @@
 # but extensions need to declare what service interface the provider intends to use for new Viewers.
 # for example,  lphystudio.app.graphicalmodelpanel.viewer.???Viewer
 
-popsizefunc.lphystudio.viewer.PopSizeFuncViewer
+# popsizefunc.lphystudio.viewer.PopSizeFuncViewer
+readcountmodel.lphystudio.viewer.ReadCountModelViewer

phylonco-lphy/examples/gt16ReadCountModel.lphy

@@ -7,10 +7,10 @@ l = 5;
 rates ~ Dirichlet(conc=[1.0, 2.0, 1.0, 1.0, 2.0, 1.0]);
 Q = gt16(freq=π, rates=rates); // construct the GT16 instantaneous rate matrix
 A ~ PhyloCTMC(L=l, Q=Q, tree=ψ, dataType=phasedGenotype());
-epsilon ~ Beta(alpha=2, beta=18);
-delta ~ Beta(alpha=1.5, beta=4.5);
-//epsilon = 0.01;
-//delta = 0.24;
+//epsilon ~ Beta(alpha=2, beta=18);
+//delta ~ Beta(alpha=1.5, beta=4.5);
+epsilon = 0.01;
+delta = 0.24;
 // cov = [rep(1, 5), rep(2, 5), rep(3, 5), rep(4, 5)];
 meanT = 2.3; // average coverage = lognormal(meanT, sdT)
 sdT = 0.1;
@@ -20,9 +20,9 @@ meanS = 0.04; // cell-specific scaling
 sdS = 0.001;
 t ~ LogNormal(meanlog= meanT, sdlog= sdT);
 v ~ LogNormal(meanlog= meanV, sdlog= sdV);
-s ~ LogNormal(meanlog= meanS, sdlog= sdS,repe);
-alpha ~ AlphaSimulator(l= l, n=n, delta= delta);
-coverage ~ CoverageSimulator(alpha= alpha, t= t, v= v, s= s);
+s ~ LogNormal(meanlog= meanS, sdlog= sdS, replicates=n);
+alpha ~ Ploidy(l= l, n= n, delta= delta);
+cov ~ CoverageModel(alpha= alpha, t= t, v= v, s= s);
 
 
-r ~ ReadCountModel(D=A, epsilon=epsilon, alpha=alpha, coverage=coverage);
+r ~ ReadCountModel(D=A, epsilon=epsilon, alpha=alpha, coverage=cov);

phylonco-lphy/src/main/java/module-info.java

@@ -4,6 +4,7 @@
 module phylonco.lphy {
     requires transitive lphy.core;
     requires transitive lphy.base;
+    requires jdk.jfr;
 
     exports phylonco.lphy.evolution.alignment;
     exports phylonco.lphy.evolution.datatype;

phylonco-lphy/src/main/java/phylonco/lphy/evolution/readcountmodel/CoverageSimulator.java → phylonco-lphy/src/main/java/phylonco/lphy/evolution/readcountmodel/CoverageModel.java

@@ -1,20 +1,20 @@
 package phylonco.lphy.evolution.readcountmodel;
 
 import lphy.base.distribution.NegativeBinomial;
-import lphy.base.evolution.alignment.Alignment;
 import lphy.core.model.GenerativeDistribution;
 import lphy.core.model.RandomVariable;
 import lphy.core.model.Value;
+import lphy.core.model.annotation.GeneratorInfo;
 import lphy.core.model.annotation.ParameterInfo;
 
 import java.util.Map;
 
-public class CoverageSimulator implements GenerativeDistribution<Integer[][]> {
+public class CoverageModel implements GenerativeDistribution<Integer[][]> {
     private NegativeBinomial negativeBinomial;
     private Value<Integer[][]> alpha;
-    private Value<Integer> t;
-    private Value<Integer> v;
-    private Value<Integer[]> s;
+    private Value<Double> t;
+    private Value<Double> v;
+    private Value<Double[]> s;
     private RandomVariable<Integer[][]> coverage;
 
 
@@ -26,11 +26,11 @@ public class CoverageSimulator implements GenerativeDistribution<Integer[][]> {
     public static final String sParamName = "s";
 
 
-    public CoverageSimulator(
+    public CoverageModel(
             @ParameterInfo(name = alphaParamName, description = "alpha, allelic dropout events for each cell at each site.") Value<Integer[][]> alpha,
-            @ParameterInfo(name = tParamName, description = "t") Value<Integer> t,
-            @ParameterInfo(name = vParamName, description = "v") Value<Integer> v,
-            @ParameterInfo(name = sParamName, description = "s") Value<Integer[]> s
+            @ParameterInfo(name = tParamName, description = "t, mean of allelic coverage.") Value<Double> t,
+            @ParameterInfo(name = vParamName, description = "v, variance of allelic coverage.") Value<Double> v,
+            @ParameterInfo(name = sParamName, description = "s, size factor of cell.") Value<Double[]> s
 
             ) {
         super();
@@ -42,6 +42,10 @@ public CoverageSimulator(
 
     }
 
+
+    @GeneratorInfo(
+            name = "CoverageModel",
+            description = "")
     @Override
     public RandomVariable<Integer[][]> sample(){
         int n = alpha.value().length;

phylonco-lphy/src/main/java/phylonco/lphy/evolution/readcountmodel/AlphaSimulator.java → phylonco-lphy/src/main/java/phylonco/lphy/evolution/readcountmodel/PloidyModel.java

@@ -1,30 +1,27 @@
 package phylonco.lphy.evolution.readcountmodel;
 
+import lphy.base.distribution.Multinomial;
 import lphy.core.model.GenerativeDistribution;
 import lphy.core.model.RandomVariable;
 import lphy.core.model.Value;
+import lphy.core.model.annotation.GeneratorInfo;
 import lphy.core.model.annotation.ParameterInfo;
 
 import java.util.Map;
 
-public class AlphaSimulator implements GenerativeDistribution<Integer[][]>  {
+public class PloidyModel implements GenerativeDistribution<Integer[][]>  {
     private Value<Integer> l;
     private Value<Integer> n;
     private Value<Double> delta;
 
     private RandomVariable<Integer[][]> alpha;
 
-
-
     public static final String lParamName = "l";
     public static final String nParamName = "n";
     public static final String deltaParamName = "delta";
 
-
-
-
-    private AlphaSimulator(
-            @ParameterInfo(name = lParamName, description = "the length of sequencing") Value<Integer> l,
+    public PloidyModel(
+            @ParameterInfo(name = lParamName, description = "the length of sequencing.") Value<Integer> l,
             @ParameterInfo(name = nParamName, description = "the number of cells.") Value<Integer> n,
             @ParameterInfo(name = deltaParamName, description = "allelic dropout error probability.") Value<Double> delta
 
@@ -34,9 +31,12 @@ private AlphaSimulator(
         this.n = n;
         this.delta = delta;
 
+    }
 
+    @GeneratorInfo(
+            name = "Ploidy",
+            description = "Observed ploidy after allelic dropout.")
 
-    }
 
     @Override
     public RandomVariable<Integer[][]> sample() {
@@ -46,9 +46,9 @@ public RandomVariable<Integer[][]> sample() {
         Value<Integer> numberA = new Value<>("numberA", 1);
         multinomialAlpha = new Multinomial(numberA, proA);
 
-        Integer[][] alp = new Integer[n.value()][l.value()];
-        for (int i = 0; i < n.value(); i++) {
-            for (int j = 0; j < l.value(); j++) {
+        Integer[][] alp = new Integer[this.n.value()][this.l.value()];
+        for (int i = 0; i < this.n.value(); i++) {
+            for (int j = 0; j < this.l.value(); j++) {
                 Value<Integer[]> alpha1 = multinomialAlpha.sample();
                 if (alpha1.value()[0] == 1) {
                     alp[i][j] = 1;

phylonco-lphy/src/main/java/phylonco/lphy/evolution/readcountmodel/ReadCountData.java

@@ -50,17 +50,20 @@ public int getDimension() {
 
     @Override
     public String toString() {
-        String result = "";
+        String result = "\n";
         int n = getTaxa().getDimension();;
         int l = nchar();
         for (int i = 0; i < n; i++) {
+            // n taxa
             for (int j = 0; j < l; j++) {
+                // n sites
                 int countA = readCountDataMatrix[i][j].getCount("A");
                 int countC = readCountDataMatrix[i][j].getCount("C");
                 int countG = readCountDataMatrix[i][j].getCount("G");
                 int countT = readCountDataMatrix[i][j].getCount("T");
                 result += String.format("A: %d, C: %d, G: %d, T: %d; \t", countA, countC, countG, countT);
             }
+            result += "\n";
         }
         return result;
     }