efischer/BiGpairSEQ
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eugenefischer
2022-09-25 16:10:17 -05:00
parent 475bbf3107
commit 58fa140ee5
2 changed files with 8 additions and 4 deletions
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6
src/main/java/GraphModificationFunctions.java
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@@ -8,7 +8,7 @@ import java.util.Map;
public interface GraphModificationFunctions {
//remove over- and under-weight edges
//remove over- and under-weight edges, return removed edges
static Map<Vertex[], Integer> filterByOverlapThresholds(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
int low, int high, boolean saveEdges) {
Map<Vertex[], Integer> removedEdges = new HashMap<>();
@@ -35,7 +35,7 @@ public interface GraphModificationFunctions {
return removedEdges;
}
//Remove edges for pairs with large occupancy discrepancy
//Remove edges for pairs with large occupancy discrepancy, return removed edges
static Map<Vertex[], Integer> filterByRelativeOccupancy(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
Integer maxOccupancyDifference, boolean saveEdges) {
Map<Vertex[], Integer> removedEdges = new HashMap<>();
@@ -63,7 +63,7 @@ public interface GraphModificationFunctions {
return removedEdges;
}
//Remove edges for pairs where overlap size is significantly lower than the well occupancy
//Remove edges for pairs where overlap size is significantly lower than the well occupancy, return removed edges
static Map<Vertex[], Integer> filterByOverlapPercent(SimpleWeightedGraph<Vertex, DefaultWeightedEdge> graph,
Integer minOverlapPercent,
boolean saveEdges) {

6
src/main/java/Simulator.java
View File

@@ -47,7 +47,7 @@ public class Simulator implements GraphModificationFunctions {
if(verbose){System.out.println("All betas count: " + betaCount);}
if(verbose){System.out.println("Well maps made");}
//ideally we wouldn't do any graph pre-filtering. But sequences present in all wells add a huge number of edges to the graph and don't carry any signal value
if(verbose){System.out.println("Removing sequences present in all wells.");}
filterByOccupancyThresholds(allAlphas, 1, numWells - 1);
filterByOccupancyThresholds(allBetas, 1, numWells - 1);
@@ -105,7 +105,9 @@ public class Simulator implements GraphModificationFunctions {
Vertex alphaVertex = new Vertex(SequenceType.CDR3_ALPHA, seq, alphaWellCounts.get(seq), plateAtoVMap.get(seq));
alphaVertices.add(alphaVertex);
}
//Sort to make sure the order of vertices in list matches the order of the adjacency matrix
Collections.sort(alphaVertices);
//Add ordered list of vertices to the graph
graphGenerator.first(alphaVertices);
//the list of beta vertices
//List<Integer> betaVertices = new ArrayList<>(plateVtoBMap.keySet());//This will work because LinkedHashMap preserves order of entry
@@ -114,7 +116,9 @@ public class Simulator implements GraphModificationFunctions {
Vertex betaVertex = new Vertex(SequenceType.CDR3_BETA, seq, betaWellCounts.get(seq), plateBtoVMap.get(seq));
betaVertices.add(betaVertex);
}
//Sort to make sure the order of vertices in list matches the order of the adjacency matrix
Collections.sort(betaVertices);
//Add ordered list of vertices to the graph
graphGenerator.second(betaVertices);
//use adjacency matrix of weight created previously
graphGenerator.weights(weights);