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Relocate overlap threshold filters

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This commit is contained in:
efischer
2022-02-20 03:05:56 -06:00
parent cb2c5a6024
commit d1c37b5ccd
4 changed files with 42 additions and 57 deletions
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BIN
out/artifacts/TCellSim_jar/TCellSim.jar
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14
src/main/java/GraphWithMapData.java
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@@ -14,8 +14,6 @@ public class GraphWithMapData implements java.io.Serializable {
private Integer[] wellConcentrations;
private Integer alphaCount;
private Integer betaCount;
private Integer lowThreshold;
private Integer highThreshold;
private final Map<Integer, Integer> distCellsMapAlphaKey;
private final Map<Integer, Integer> plateVtoAMap;
private final Map<Integer, Integer> plateVtoBMap;
@@ -26,7 +24,7 @@ public class GraphWithMapData implements java.io.Serializable {
private final Duration time;
public GraphWithMapData(SimpleWeightedGraph graph, Integer numWells, Integer[] wellConcentrations,
Integer alphaCount, Integer betaCount, Integer lowThreshold, Integer highThreshold,
Integer alphaCount, Integer betaCount,
Map<Integer, Integer> distCellsMapAlphaKey, Map<Integer, Integer> plateVtoAMap,
Map<Integer,Integer> plateVtoBMap, Map<Integer, Integer> plateAtoVMap,
Map<Integer, Integer> plateBtoVMap, Map<Integer, Integer> alphaWellCounts,
@@ -36,8 +34,6 @@ public class GraphWithMapData implements java.io.Serializable {
this.wellConcentrations = wellConcentrations;
this.alphaCount = alphaCount;
this.betaCount = betaCount;
this.lowThreshold = lowThreshold;
this.highThreshold = highThreshold;
this.distCellsMapAlphaKey = distCellsMapAlphaKey;
this.plateVtoAMap = plateVtoAMap;
this.plateVtoBMap = plateVtoBMap;
@@ -68,14 +64,6 @@ public class GraphWithMapData implements java.io.Serializable {
return betaCount;
}
public Integer getLowThreshold() {
return lowThreshold;
}
public Integer getHighThreshold() {
return highThreshold;
}
public Map<Integer, Integer> getDistCellsMapAlphaKey() {
return distCellsMapAlphaKey;
}

27
src/main/java/Simulator.java
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@@ -45,8 +45,7 @@ public class Simulator {
}
//Make the graph needed for matching CDR3s
public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, Integer lowThreshold,
Integer highThreshold, boolean verbose) {
public static GraphWithMapData makeGraph(List<Integer[]> distinctCells, Plate samplePlate, boolean verbose) {
Instant start = Instant.now();
int[] alphaIndex = {cdr3AlphaIndex};
int[] betaIndex = {cdr3BetaIndex};
@@ -70,9 +69,9 @@ public class Simulator {
//Remove saturating-occupancy sequences because they have no signal value.
//Remove sequences with total occupancy below minimum pair overlap threshold
if(verbose){System.out.println("Removing sequences present in all wells.");}
if(verbose){System.out.println("Removing sequences with occupancy below the minimum overlap threshold");}
filterByOccupancyThreshold(allAlphas, lowThreshold, numWells - 1);
filterByOccupancyThreshold(allBetas, lowThreshold, numWells - 1);
//if(verbose){System.out.println("Removing sequences with occupancy below the minimum overlap threshold");}
filterByOccupancyThreshold(allAlphas, 1, numWells - 1);
filterByOccupancyThreshold(allBetas, 1, numWells - 1);
if(verbose){System.out.println("Sequences removed");}
int pairableAlphaCount = allAlphas.size();
if(verbose){System.out.println("Remaining alphas count: " + pairableAlphaCount);}
@@ -130,25 +129,20 @@ public class Simulator {
graphGenerator.generateGraph(graph);
if(verbose){System.out.println("Graph created");}
//remove weights outside given overlap thresholds
if(verbose){System.out.println("Eliminating edges with weights outside overlap threshold values");}
filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
if(verbose){System.out.println("Over- and under-weight edges set to 0.0");}
Instant stop = Instant.now();
Duration time = Duration.between(start, stop);
//return GraphWithMapData object
return new GraphWithMapData(graph, numWells, samplePlate.getConcentrations(), alphaCount, betaCount, lowThreshold, highThreshold,
return new GraphWithMapData(graph, numWells, samplePlate.getConcentrations(), alphaCount, betaCount,
distCellsMapAlphaKey, plateVtoAMap, plateVtoBMap, plateAtoVMap,
plateBtoVMap, alphaWellCounts, betaWellCounts, time);
}
//match CDR3s.
public static MatchingResult matchCDR3s(GraphWithMapData data, Integer maxOccupancyDifference,
Integer minOverlapPercent, boolean verbose) {
public static MatchingResult matchCDR3s(GraphWithMapData data, Integer lowThreshold, Integer highThreshold,
Integer maxOccupancyDifference, Integer minOverlapPercent,
boolean verbose) {
Instant start = Instant.now();
int numWells = data.getNumWells();
Integer highThreshold = data.getHighThreshold();
Integer lowThreshold = data.getLowThreshold();
Integer alphaCount = data.getAlphaCount();
Integer betaCount = data.getBetaCount();
Map<Integer, Integer> distCellsMapAlphaKey = data.getDistCellsMapAlphaKey();
@@ -158,6 +152,11 @@ public class Simulator {
Map<Integer, Integer> betaWellCounts = data.getBetaWellCounts();
SimpleWeightedGraph<Integer, DefaultWeightedEdge> graph = data.getGraph();
//remove weights outside given overlap thresholds
if(verbose){System.out.println("Eliminating edges with weights outside overlap threshold values");}
filterByOccupancyThreshold(graph, lowThreshold, highThreshold);
if(verbose){System.out.println("Over- and under-weight edges set to 0.0");}
//Filter by overlap size
if(verbose){System.out.println("Eliminating edges with weights less than " + minOverlapPercent.toString() +
" percent of vertex occupancy value.");}

58
src/main/java/UserInterface.java
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@@ -303,10 +303,10 @@ public class UserInterface {
System.out.println("\nThe cells will be written to a CSV file.");
System.out.print("Please enter a file name: ");
filename = sc.next();
System.out.println("CDR3 sequences are more diverse than CDR1 sequences.");
System.out.println("\nCDR3 sequences are more diverse than CDR1 sequences.");
System.out.println("Please enter the factor by which distinct CDR3s outnumber CDR1s: ");
cdr1Freq = sc.nextInt();
System.out.print("Please enter the number of T-cells to generate: ");
System.out.print("\nPlease enter the number of T-cells to generate: ");
numCells = sc.nextInt();
if(numCells <= 0){
throw new InputMismatchException("Number of cells must be a positive integer.");
@@ -380,7 +380,7 @@ public class UserInterface {
System.out.println("\nThe sample plate will be written to a CSV file");
System.out.print("Please enter a name for the output file: ");
filename = sc.next();
System.out.println("Select T-cell frequency distribution function");
System.out.println("\nSelect T-cell frequency distribution function");
System.out.println("1) Poisson");
System.out.println("2) Gaussian");
System.out.println("3) Exponential");
@@ -413,12 +413,12 @@ public class UserInterface {
System.out.println("Invalid input. Defaulting to exponential.");
exponential = true;
}
System.out.print("Number of wells on plate: ");
System.out.print("\nNumber of wells on plate: ");
numWells = sc.nextInt();
if(numWells < 1){
throw new InputMismatchException("No wells on plate");
}
System.out.println("The plate can be evenly sectioned to allow multiple concentrations of T-cells/well");
System.out.println("\nThe plate can be evenly sectioned to allow multiple concentrations of T-cells/well");
System.out.println("How many sections would you like to make (minimum 1)?");
numSections = sc.nextInt();
if(numSections < 1) {
@@ -435,7 +435,7 @@ public class UserInterface {
i++;
numSections--;
}
System.out.println("Errors in amplification can induce a well dropout rate for sequences");
System.out.println("\nErrors in amplification can induce a well dropout rate for sequences");
System.out.print("Enter well dropout rate (0.0 to 1.0): ");
dropOutRate = sc.nextDouble();
if(dropOutRate < 0.0 || dropOutRate > 1.0) {
@@ -468,26 +468,18 @@ public class UserInterface {
String filename = null;
String cellFile = null;
String plateFile = null;
Integer lowThreshold = 0;
Integer highThreshold = Integer.MAX_VALUE;
try {
String str = "\nGenerating bipartite weighted graph encoding occupancy overlap data ";
str = str.concat("\nrequires a cell sample file and a sample plate file.");
System.out.println(str);
System.out.print("Please enter name of an existing cell sample file: ");
System.out.print("\nPlease enter name of an existing cell sample file: ");
cellFile = sc.next();
System.out.print("Please enter name of an existing sample plate file: ");
System.out.print("\nPlease enter name of an existing sample plate file: ");
plateFile = sc.next();
System.out.println("The graph and occupancy data will be written to a serialized binary file.");
System.out.println("\nThe graph and occupancy data will be written to a serialized binary file.");
System.out.print("Please enter a name for the output file: ");
filename = sc.next();
System.out.println("What is the minimum number of CDR3 alpha/beta overlap wells to include in graph?");
lowThreshold = sc.nextInt();
if(lowThreshold < 1){
throw new InputMismatchException("Minimum value for low threshold set to 1");
}
System.out.println("What is the maximum number of CDR3 alpha/beta overlap wells to include in graph?");
highThreshold = sc.nextInt();
} catch (InputMismatchException ex) {
System.out.println(ex);
sc.next();
@@ -504,11 +496,9 @@ public class UserInterface {
System.out.println("Returning to main menu.");
}
else{
if(highThreshold >= plate.getSize()){
highThreshold = plate.getSize() - 1;
}
List<Integer[]> cells = cellReader.getCells();
GraphWithMapData data = Simulator.makeGraph(cells, plate, lowThreshold, highThreshold, true);
GraphWithMapData data = Simulator.makeGraph(cells, plate, true);
GraphDataObjectWriter dataWriter = new GraphDataObjectWriter(filename, data);
System.out.println("Writing graph and occupancy data to file. This may take some time.");
System.out.println("File I/O time is not included in results.");
@@ -520,6 +510,8 @@ public class UserInterface {
private static void matchCDR3s() throws IOException {
String filename = null;
String dataFile = null;
Integer lowThreshold = 0;
Integer highThreshold = Integer.MAX_VALUE;
Integer maxOccupancyDiff = Integer.MAX_VALUE;
Integer minOverlapPercent = 0;
try {
@@ -529,13 +521,18 @@ public class UserInterface {
System.out.println("The matching results will be written to a file.");
System.out.print("Please enter a name for the output file: ");
filename = sc.next();
System.out.println("Bipartite graph can be pre-filtered for relative alpha/beta occupancy.");
System.out.println("(To skip pre-filtering: enter number of wells on the plate used to make graph)");
System.out.println("What is the maximum difference in alpha/beta occupancy to attempt matching?");
filename = sc.next();
System.out.println("\nWhat is the minimum number of CDR3 alpha/beta overlap wells to attempt matching?");
lowThreshold = sc.nextInt();
if(lowThreshold < 1){
throw new InputMismatchException("Minimum value for low threshold set to 1");
}
System.out.println("\nWhat is the maximum number of CDR3 alpha/beta overlap wells to attempt matching?");
highThreshold = sc.nextInt();
System.out.println("\nWhat is the maximum difference in alpha/beta occupancy to attempt matching?");
maxOccupancyDiff = sc.nextInt();
System.out.println("Bipartite graph can be pre-filtered for pair well overlap percentage");
System.out.println("(To skip pre-filtering: enter 0)");
System.out.println("What is the minimum overlap percentage to attempt matching? (0 - 100)");
System.out.println("\nWell overlap percentage = pair overlap / sequence occupancy");
System.out.println("What is the minimum well overlap percentage to attempt matching? (0 to 100)");
minOverlapPercent = sc.nextInt();
if (minOverlapPercent < 0 || minOverlapPercent > 100) {
throw new InputMismatchException("Value outside range. Minimum percent set to 0");
@@ -552,7 +549,8 @@ public class UserInterface {
//set source file name
data.setSourceFilename(dataFile);
//simulate matching
MatchingResult results = Simulator.matchCDR3s(data, maxOccupancyDiff, minOverlapPercent, true);
MatchingResult results = Simulator.matchCDR3s(data, lowThreshold, highThreshold, maxOccupancyDiff,
minOverlapPercent, true);
//write results to file
MatchingFileWriter writer = new MatchingFileWriter(filename, results);
System.out.println("Writing results to file");