Add signature data sets to creation parameters dialog. Refs #308

Author: mikekucera

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/commands/PAKnownSignatureCommandTask.java

@@ -139,7 +139,9 @@ public void run(TaskMonitor taskMonitor) throws Exception {
 			.setAttributePrefix(map.getParams().getAttributePrefix())
 			.setLoadedGMTGeneSets(signatureGenesets)
 			.addSelectedGeneSetNames(selectedGenesetNames)
-			.setName(Strings.isNullOrEmpty(name) ? autoName : name);
+			.setName(Strings.isNullOrEmpty(name) ? autoName : name)
+			.setSource(PostAnalysisParameters.SOURCE_LOCAL_FILE)
+			.setGmtFile(gmtFile.getPath());
 
 		if(isBatch()) {
 			builder.setDataSetName(null); // run in batch mode
@@ -205,7 +207,7 @@ private FilterMetric.MannWhit processMannWhitneyArgs(EnrichmentMap map, EMDataSe
 		if(mannWhitRanks.isEmpty() && map.isSingleRanksPerDataset()) {
 			String ranksName = dataset.getAllRanksNames().iterator().next();
 			Ranking ranking = dataset.getRanksByName(ranksName);
-			return new FilterMetric.MannWhit(cutoff, ranking, type);
+			return new FilterMetric.MannWhit(cutoff, ranksName, ranking, type);
 		} else if(mannWhitRanks.isEmpty()) {
 			throw new IllegalArgumentException("At least one of the data sets you have specified has more than one ranks file. "
 					+ "You must use the 'mannWhitRanks' parameter to specify which ranking to use for each data set.");
@@ -224,10 +226,10 @@ private FilterMetric.MannWhit processMannWhitneyArgs(EnrichmentMap map, EMDataSe
 			if(rankFile == null && ranksNames.size() == 1) {
 				String ranksName = ranksNames.iterator().next();
 				Ranking ranking = dataset.getRanksByName(ranksName);
-				return new FilterMetric.MannWhit(cutoff, ranking, type);
+				return new FilterMetric.MannWhit(cutoff, ranksName, ranking, type);
 			} else {
 				Ranking ranking = dataset.getRanksByName(rankFile);
-				return new FilterMetric.MannWhit(cutoff, ranking, type);
+				return new FilterMetric.MannWhit(cutoff, rankFile, ranking, type);
 			}
 		}
 	}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/EMSignatureDataSet.java

@@ -1,11 +1,57 @@
 package org.baderlab.csplugins.enrichmentmap.model;
 
+import java.util.Map;
+
+import javax.annotation.Nullable;
+
 public class EMSignatureDataSet extends AbstractDataSet {
 
+	// These fields were added in 3.1, sessions saved with 3.0 will not be able to restore these fields.
+	// These are just to remember some of the creation parameters to show in the Creation Paramters Dialog.
+	private @Nullable String source;
+	private @Nullable String gmtFile;
+	private @Nullable PostAnalysisFilterType type;
+	private @Nullable Map<String,String> dataSetRankTestMessage;
+	
+	
 	public EMSignatureDataSet(EnrichmentMap map, String name) {
 		super(map, name);
 	}
 
+	
+	public String getSource() {
+		return source;
+	}
+
+	public void setSource(String source) {
+		this.source = source;
+	}
+
+	public String getGmtFile() {
+		return gmtFile;
+	}
+
+	public void setGmtFile(String gmtFile) {
+		this.gmtFile = gmtFile;
+	}
+
+	public PostAnalysisFilterType getType() {
+		return type;
+	}
+
+	public void setType(PostAnalysisFilterType type) {
+		this.type = type;
+	}
+
+	public Map<String, String> getDataSetRankTestMessage() {
+		return dataSetRankTestMessage;
+	}
+
+	public void setDataSetRankTestMessage(Map<String, String> dataSetRankTestMessage) {
+		this.dataSetRankTestMessage = dataSetRankTestMessage;
+	}
+
+
 	@Override
 	public int hashCode() {
 		final int prime = 11;

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/model/PostAnalysisParameters.java

@@ -52,6 +52,8 @@
 
 public class PostAnalysisParameters {
 
+	public static final String SOURCE_LOCAL_FILE = "local file";
+	
 	final public static String SIGNATURE_INTERACTION_TYPE = "sig";
 	@Deprecated
 	final public static String SIGNATURE_INTERACTION_TYPE_SET1 = "sig_set1";
@@ -65,6 +67,8 @@ public class PostAnalysisParameters {
 	private final Collection<String> selectedGeneSetNames;
 	private final String attributePrefix;
 	private final Optional<String> datasetName;
+	private final String source;
+	private final String gmtFile;
 
 	private PostAnalysisParameters(PostAnalysisParameters.Builder builder) {
 		this.name = builder.name;
@@ -73,6 +77,8 @@ private PostAnalysisParameters(PostAnalysisParameters.Builder builder) {
 		this.selectedGeneSetNames = builder.selectedGeneSetNames;
 		this.attributePrefix = builder.attributePrefix;
 		this.datasetName = builder.datasetName;
+		this.source = builder.source;
+		this.gmtFile = builder.gmtFile;
 	}
 
 	public String getName() {
@@ -98,6 +104,14 @@ public Collection<String> getSelectedGeneSetNames() {
 	public String getAttributePrefix() {
 		return attributePrefix;
 	}
+	
+	public String getSource() {
+		return source;
+	}
+	
+	public String getGmtFile() {
+		return gmtFile;
+	}
 
 
 	public static class Builder {
@@ -108,7 +122,8 @@ public static class Builder {
 		private Set<String> selectedGeneSetNames = new HashSet<>();
 		private String attributePrefix;
 		private Optional<String> datasetName = Optional.empty();
-		
+		private String source;
+		private String gmtFile;
 
 		public static Builder from(PostAnalysisParameters other) {
 			Builder b = new Builder();
@@ -118,6 +133,8 @@ public static Builder from(PostAnalysisParameters other) {
 			b.addSelectedGeneSetNames(other.selectedGeneSetNames);
 			b.setAttributePrefix(other.attributePrefix);
 			b.setDataSetName(other.datasetName.orElse(null));
+			b.setSource(other.source);
+			b.setGmtFile(other.gmtFile);
 			return b;
 		}
 
@@ -160,6 +177,16 @@ public Builder setAttributePrefix(String attributePrefix) {
 			return this;
 		}
 
+		public Builder setSource(String source) {
+			this.source = source;
+			return this;
+		}
+		
+		public Builder setGmtFile(String gmtFile) {
+			this.gmtFile = gmtFile;
+			return this;
+		}
+		
 		public PostAnalysisParameters build() {
 			return new PostAnalysisParameters(this);
 		}

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/postanalysis/CreatePANetworkTask.java

@@ -144,7 +144,23 @@ public void run(TaskMonitor tm) {
 	 */
 	private EMSignatureDataSet createSignatureDataSet() {
 		String name = params.getName();
-		return new EMSignatureDataSet(map, name);
+		EMSignatureDataSet sigDataSet = new EMSignatureDataSet(map, name);
+		
+		// set fields that show up in the Creation Parameters dialog
+		sigDataSet.setSource(params.getSource());
+		sigDataSet.setGmtFile(params.getGmtFile());
+		
+		FilterMetricSet rankTestParams = params.getRankTestParameters();
+		sigDataSet.setType(rankTestParams.getType());
+		
+		Map<String,String> dataSetMessages = new HashMap<>();
+		for(String dataSetName : rankTestParams.getDataSetNames()) {
+			FilterMetric metric = rankTestParams.get(dataSetName);
+			dataSetMessages.put(dataSetName, metric.getDisplayString());
+		}
+		sigDataSet.setDataSetRankTestMessage(dataSetMessages);
+		
+		return sigDataSet;
 	}
 
 

EnrichmentMapPlugin/src/main/java/org/baderlab/csplugins/enrichmentmap/task/postanalysis/FilterMetric.java

@@ -29,6 +29,8 @@ public interface FilterMetric {
 
 	double moreSimilar(double x, double y);
 
+	String getDisplayString();
+	
 
 	abstract class BaseFilterMetric implements FilterMetric {
 		protected final double cutoff;
@@ -71,6 +73,10 @@ public double computeValue(Set<Integer> geneSet, Set<Integer> sigSet, @Nullable
 			return 0;
 		}
 
+		public String getDisplayString() {
+			return "no filter";
+		}
+		
 	}
 
 
@@ -92,6 +98,10 @@ public double computeValue(Set<Integer> geneSet, Set<Integer> sigSet, @Nullable
 			Set<Integer> intersection = Sets.intersection(geneSet, sigSet);
 			return (double) intersection.size() / (double) geneSet.size();
 		}
+		
+		public String getDisplayString() {
+			return "(intersection size)/(gene set size) >= " + (cutoff / 100.0);
+		}
 	}
 
 
@@ -112,6 +122,10 @@ public double moreSimilar(double x, double y) {
 		public double computeValue(Set<Integer> geneSet, Set<Integer> sigSet, @Nullable SignatureGenesetSimilarity similarity) {
 			return Sets.intersection(geneSet, sigSet).size();
 		}
+		
+		public String getDisplayString() {
+			return "intersection size >= " + cutoff;
+		}
 	}
 
 
@@ -133,6 +147,10 @@ public double computeValue(Set<Integer> geneSet, Set<Integer> sigSet, @Nullable
 			Set<Integer> intersection = Sets.intersection(geneSet, sigSet);
 			return (double) intersection.size() / (double) sigSet.size();
 		}
+		
+		public String getDisplayString() {
+			return "(intersection size)/(signature gene set size) >= " + (cutoff / 100.0);
+		}
 	}
 
 
@@ -177,20 +195,26 @@ public double computeValue(Set<Integer> geneSet, Set<Integer> sigSet, @Nullable
 
 			return hyperPval;
 		}
+		
+		public String getDisplayString() {
+			return "universe size = " + u;
+		}
 	}
 
 
 	class MannWhit extends BaseFilterMetric {
 
+		private final String rankingName;
 		private final Ranking ranks;
 		private final MannWhitneyMemoized mannWhitneyCache = new MannWhitneyMemoized();
 
 
-		public MannWhit(double filter, Ranking ranks, PostAnalysisFilterType type) {
+		public MannWhit(double filter, String rankingName, Ranking ranks, PostAnalysisFilterType type) {
 			super(type, filter);
 			if(!type.isMannWhitney())
 				throw new IllegalArgumentException("FilterType is not Mann Whitney: " + type);
 			this.ranks = ranks;
+			this.rankingName = rankingName;
 		}
 
 		public boolean passes(double value) {
@@ -246,6 +270,10 @@ public double computeValue(Set<Integer> geneSet, Set<Integer> sigSet, @Nullable
 				}
 			}
 		}
+		
+		public String getDisplayString() {
+			return "ranks: " + rankingName;
+		}
 	}