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Implement read count for vertices

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eugenefischer
2022-09-26 19:42:19 -05:00
parent 19a2a35f07
commit 199c81f983
6 changed files with 93 additions and 15 deletions
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34
src/main/java/GraphModificationFunctions.java
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@@ -12,7 +12,6 @@ public interface GraphModificationFunctions {
static Map<Vertex[], Integer> filterByOverlapThresholds(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
int low, int high, boolean saveEdges) {
Map<Vertex[], Integer> removedEdges = new HashMap<>();
//List<Integer[]> removedEdges = new ArrayList<>();
for (DefaultWeightedEdge e : graph.edgeSet()) {
if ((graph.getEdgeWeight(e) > high) || (graph.getEdgeWeight(e) < low)) {
if(saveEdges) {
@@ -94,6 +93,37 @@ public interface GraphModificationFunctions {
return removedEdges;
}
static Map<Vertex[], Integer> filterByRelativeReadCount (SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph, Integer threshold, boolean saveEdges) {
Map<Vertex[], Integer> removedEdges = new HashMap<>();
Boolean passes;
for (DefaultWeightedEdge e : graph.edgeSet()) {
Integer alphaReadCount = graph.getEdgeSource(e).getReadCount();
Integer betaReadCount = graph.getEdgeTarget(e).getReadCount();
passes = RelativeReadCountFilterFunction(threshold, alphaReadCount, betaReadCount);
if (!passes) {
if (saveEdges) {
Vertex source = graph.getEdgeSource(e);
Vertex target = graph.getEdgeTarget(e);
Integer intWeight = (int) graph.getEdgeWeight(e);
Vertex[] edge = {source, target};
removedEdges.put(edge, intWeight);
}
else {
graph.setEdgeWeight(e, 0.0);
}
}
}
if(saveEdges) {
for (Vertex[] edge : removedEdges.keySet()) {
graph.removeEdge(edge[0], edge[1]);
}
}
return removedEdges;
}
static Boolean RelativeReadCountFilterFunction(Integer threshold, Integer alphaReadCount, Integer betaReadCount) {
return Math.abs(alphaReadCount - betaReadCount) < threshold;
}
static void addRemovedEdges(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
Map<Vertex[], Integer> removedEdges) {
for (Vertex[] edge : removedEdges.keySet()) {
@@ -102,4 +132,6 @@ public interface GraphModificationFunctions {
}
}
}

5
src/main/java/GraphWithMapData.java
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@@ -15,6 +15,7 @@ public class GraphWithMapData implements java.io.Serializable {
private Integer[] wellPopulations;
private Integer alphaCount;
private Integer betaCount;
private int readDepth;
private final Map<String, String> distCellsMapAlphaKey;
// private final Map<Integer, Integer> plateVtoAMap;
// private final Map<Integer, Integer> plateVtoBMap;
@@ -25,7 +26,7 @@ public class GraphWithMapData implements java.io.Serializable {
private final Duration time;
public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer[] wellConcentrations,
Map<String, String> distCellsMapAlphaKey, Integer alphaCount, Integer betaCount, Duration time){
Map<String, String> distCellsMapAlphaKey, Integer alphaCount, Integer betaCount, int readDepth, Duration time){
// Map<Integer, Integer> plateVtoAMap,
// Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
@@ -94,6 +95,8 @@ public class GraphWithMapData implements java.io.Serializable {
// return betaWellCounts;
// }
public int getReadDepth() { return readDepth; }
public Duration getTime() {
return time;
}

5
src/main/java/InteractiveInterface.java
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@@ -273,6 +273,9 @@ public class InteractiveInterface {
if (simulateReadDepth) {
System.out.print("\nPlease enter read depth (the integer number of reads per sequence): ");
readDepth = sc.nextInt();
if(readDepth < 1) {
throw new InputMismatchException("The read depth must be an integer >= 1");
}
System.out.print("\nPlease enter probability of a sequence read error (0.0 to 1.0): ");
readErrorRate = sc.nextDouble();
if(readErrorRate < 0.0 || readErrorRate > 1.0) {
@@ -332,7 +335,7 @@ public class InteractiveInterface {
System.out.println("Returning to main menu.");
}
else{
GraphWithMapData data = Simulator.makeGraph(cellSample, plate, true);
GraphWithMapData data = Simulator.makeGraph(cellSample, plate, readDepth, readErrorRate, errorCollisionRate, true);
assert filename != null;
if(BiGpairSEQ.outputBinary()) {
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);

21
src/main/java/Plate.java
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@@ -178,17 +178,30 @@ public class Plate {
}
}
//returns a map of the counts of the sequence at cell index sIndex, in a specific of wells
//Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
public void assayWellsSequenceSWithReadDepth(Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
int readDepth, double readErrorProb, double errorCollisionProb, int... sIndices) {
this.assayWellsSequenceSWithReadDepth(occupancyMap, readCountMap, readDepth, readErrorProb, errorCollisionProb, 0, size, sIndices);
}
//returns a map of the counts of the sequence at cell index sIndex, in a specific of wells
//Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
public void assayWellsSequenceSWithReadDepth(Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
int readDepth, double readErrorProb, double errorCollisionProb,
int n, int... sIndices) {
this.assayWellsSequenceSWithReadDepth(occupancyMap, readCountMap, readDepth, readErrorProb, errorCollisionProb, n, n+1, sIndices);
}
//returns a map of the counts of the sequence at cell index sIndex, in a range of wells
//Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.
public Map<String, Integer> assayWellsSequenceSWithReadDepth(int start, int end, int... sIndices) {
Map<String, Integer> assay = new HashMap<>();
public void assayWellsSequenceSWithReadDepth(Map<String, Integer> occupancyMap, Map<String, Integer> readCountMap,
int readDepth, double readErrorProb, double errorCollisionProb,
int start, int end, int... sIndices) {
for(int sIndex: sIndices){
for(int i = start; i < end; i++){
countSequences(assay, wells.get(i), sIndex);
countSequencesWithReadDepth(occupancyMap, readCountMap, readDepth, readErrorProb, errorCollisionProb, wells.get(i), sIndex);
}
}
return assay;
}
//For the sequences at cell indices sIndices, counts number of unique sequences in the given well into the given map
//Simulates read depth and read errors, counts the number of reads of a unique sequence into the given map.

42
src/main/java/Simulator.java
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@@ -21,8 +21,12 @@ public class Simulator implements GraphModificationFunctions {
//sourceVertexIndices and targetVertexIndices are indices within the cell to use as for the two sets of vertices
//in the bipartite graph. "Source" and "target" are JGraphT terms for the two vertices an edge touches,
//even if not directed.
public static GraphWithMapData makeGraph(CellSample cellSample, Plate samplePlate, boolean verbose) {
public static GraphWithMapData makeGraph(CellSample cellSample, Plate samplePlate, int readDepth, double readErrorRate, double errorCollisionRate, boolean verbose) {
Instant start = Instant.now();
Map<String, Integer> allAlphas;
Map<String, Integer> allBetas;
Map<String, Integer> alphaReadCounts = null;
Map<String, Integer> betaReadCounts = null;
List<String[]> distinctCells = cellSample.getCells();
int[] alphaIndices = {SequenceType.CDR3_ALPHA.ordinal()};
int[] betaIndices = {SequenceType.CDR3_BETA.ordinal()};
@@ -35,11 +39,21 @@ public class Simulator implements GraphModificationFunctions {
if(verbose){System.out.println("Cell maps made");}
if(verbose){System.out.println("Making well maps");}
if(readDepth == 1) {
allAlphas = new HashMap<>();
samplePlate.assayWellsSequenceS(allAlphas, alphaIndices);
allBetas = new HashMap<>();
samplePlate.assayWellsSequenceS(allBetas, betaIndices);
}
else {
allAlphas = new HashMap<>();
alphaReadCounts = new HashMap<>();
samplePlate.assayWellsSequenceSWithReadDepth(allAlphas, alphaReadCounts, readDepth, readErrorRate, errorCollisionRate, alphaIndices);
allBetas = new HashMap<>();
betaReadCounts = new HashMap<>();
samplePlate.assayWellsSequenceSWithReadDepth(allBetas, betaReadCounts, readDepth, readErrorRate, errorCollisionRate, betaIndices);
}
Map<String, Integer> allAlphas = new HashMap<>();
samplePlate.assayWellsSequenceS(allAlphas, alphaIndices);
Map<String, Integer> allBetas = new HashMap<>();
samplePlate.assayWellsSequenceS(allBetas, betaIndices);
int alphaCount = allAlphas.size();
if(verbose){System.out.println("All alphas count: " + alphaCount);}
int betaCount = allBetas.size();
@@ -101,7 +115,13 @@ public class Simulator implements GraphModificationFunctions {
List<Vertex> alphaVertices = new ArrayList<>();
//start with map of all alphas mapped to vertex values, get occupancy from the alphaWellCounts map
for (String seq : plateAtoVMap.keySet()) {
Vertex alphaVertex = new Vertex(SequenceType.CDR3_ALPHA, seq, alphaWellCounts.get(seq), plateAtoVMap.get(seq));
Vertex alphaVertex;
if (readDepth == 1) {
alphaVertex = new Vertex(SequenceType.CDR3_ALPHA, seq, alphaWellCounts.get(seq), plateAtoVMap.get(seq));
}
else {
alphaVertex = new Vertex(SequenceType.CDR3_ALPHA, seq, alphaWellCounts.get(seq), plateAtoVMap.get(seq), alphaReadCounts.get(seq));
}
alphaVertices.add(alphaVertex);
}
//Sort to make sure the order of vertices in list matches the order of the adjacency matrix
@@ -112,7 +132,13 @@ public class Simulator implements GraphModificationFunctions {
//List<Integer> betaVertices = new ArrayList<>(plateVtoBMap.keySet());//This will work because LinkedHashMap preserves order of entry
List<Vertex> betaVertices = new ArrayList<>();
for (String seq : plateBtoVMap.keySet()) {
Vertex betaVertex = new Vertex(SequenceType.CDR3_BETA, seq, betaWellCounts.get(seq), plateBtoVMap.get(seq));
Vertex betaVertex;
if (readDepth == 1) {
betaVertex = new Vertex(SequenceType.CDR3_BETA, seq, betaWellCounts.get(seq), plateBtoVMap.get(seq));
}
else {
betaVertex = new Vertex(SequenceType.CDR3_BETA, seq, betaWellCounts.get(seq), plateBtoVMap.get(seq), betaReadCounts.get(seq));
}
betaVertices.add(betaVertex);
}
//Sort to make sure the order of vertices in list matches the order of the adjacency matrix
@@ -128,7 +154,7 @@ public class Simulator implements GraphModificationFunctions {
Duration time = Duration.between(start, stop);
//create GraphWithMapData object
GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), distCellsMapAlphaKey, alphaCount, betaCount, time);
GraphWithMapData output = new GraphWithMapData(graph, numWells, samplePlate.getPopulations(), distCellsMapAlphaKey, alphaCount, betaCount, readDepth, time);
//Set source file name in graph to name of sample plate
output.setSourceFilename(samplePlate.getFilename());
//return GraphWithMapData object

1
src/main/java/Vertex.java
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@@ -23,6 +23,7 @@ public class Vertex implements Serializable, Comparable<Vertex> {
this.vertexLabel = vertexLabel;
this.sequence = sequence;
this.occupancy = occupancy;
this.readCount = 1;
}
public Vertex(SequenceType type, String sequence, Integer occupancy, Integer vertexLabel, Integer readCount) {