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Merge pull request #70 from VEuPathDB/add-differential-expression
add differential expression
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,40 @@ | ||
| #%RAML 1.0 Library | ||
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| types: | ||
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| DifferentialExpressionPluginRequest: | ||
| type: ComputeRequestBase | ||
| properties: | ||
| config: DifferentialExpressionComputeConfig | ||
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| DifferentialExpressionComputeConfig: | ||
| properties: | ||
| collectionVariable: CollectionSpec | ||
| comparator: ComparatorSpec | ||
| differentialExpressionMethod: DifferentialExpressionMethod | ||
| pValueFloor: | ||
| type: string | ||
| required: false | ||
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| DifferentialExpressionMethod: | ||
| type: string | ||
| enum: ['DESeq'] | ||
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| ComparatorSpec: | ||
| type: object | ||
| properties: | ||
| variable: VariableSpec | ||
| groupA: LabeledRange[] | ||
| groupB: LabeledRange[] | ||
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| DifferentialExpressionPoint: | ||
| properties: | ||
| effectSize: string | ||
| pValue: string | ||
| adjustedPValue: string | ||
| pointId: string | ||
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| DifferentialExpressionStatsResponse: | ||
| properties: | ||
| effectSizeLabel: string | ||
| statistics: DifferentialExpressionPoint[] |
9 changes: 9 additions & 0 deletions
9
schema/url/data/differentialexpression/plugin-differentialexpression-volcanoplot.raml
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| Original file line number | Diff line number | Diff line change |
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| @@ -0,0 +1,9 @@ | ||
| #%RAML 1.0 Library | ||
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| types: | ||
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| DifferentialExpressionVolcanoplotPostRequest: | ||
| type: DataPluginRequestBase | ||
| properties: | ||
| computeConfig: DifferentialExpressionComputeConfig | ||
| config: EmptyDataPluginSpec |
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152 changes: 152 additions & 0 deletions
152
...thdb/service/eda/compute/plugins/differentialexpression/DifferentialExpressionPlugin.java
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| package org.veupathdb.service.eda.compute.plugins.differentialexpression; | ||
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| import org.gusdb.fgputil.ListBuilder; | ||
| import org.jetbrains.annotations.NotNull; | ||
| import org.veupathdb.service.eda.common.client.spec.StreamSpec; | ||
| import org.veupathdb.service.eda.common.model.CollectionDef; | ||
| import org.veupathdb.service.eda.common.model.EntityDef; | ||
| import org.veupathdb.service.eda.common.model.ReferenceMetadata; | ||
| import org.veupathdb.service.eda.common.model.VariableDef; | ||
| import org.veupathdb.service.eda.common.plugin.util.PluginUtil; | ||
| import org.veupathdb.service.eda.compute.RServe; | ||
| import org.veupathdb.service.eda.compute.plugins.AbstractPlugin; | ||
| import org.veupathdb.service.eda.compute.plugins.PluginContext; | ||
| import org.veupathdb.service.eda.generated.model.LabeledRange; | ||
| import org.veupathdb.service.eda.generated.model.DifferentialExpressionComputeConfig; | ||
| import org.veupathdb.service.eda.generated.model.DifferentialExpressionPluginRequest; | ||
| import org.veupathdb.service.eda.generated.model.CollectionSpec; | ||
| import org.veupathdb.service.eda.generated.model.VariableSpec; | ||
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| import java.io.InputStream; | ||
| import java.util.ArrayList; | ||
| import java.util.HashMap; | ||
| import java.util.List; | ||
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| import static org.veupathdb.service.eda.common.plugin.util.PluginUtil.singleQuote; | ||
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| public class DifferentialExpressionPlugin extends AbstractPlugin<DifferentialExpressionPluginRequest, DifferentialExpressionComputeConfig> { | ||
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| private static final String INPUT_DATA = "differential_expression_input"; | ||
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| public DifferentialExpressionPlugin(@NotNull PluginContext<DifferentialExpressionPluginRequest, DifferentialExpressionComputeConfig> context) { | ||
| super(context); | ||
| } | ||
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| @NotNull | ||
| @Override | ||
| public List<StreamSpec> getStreamSpecs() { | ||
| return List.of(new StreamSpec(INPUT_DATA, getConfig().getCollectionVariable().getEntityId()) | ||
| .addVars(getUtil().getCollectionMembers(getConfig().getCollectionVariable())) | ||
| .addVar(getConfig().getComparator().getVariable()) | ||
| ); | ||
| } | ||
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| @Override | ||
| protected void execute() { | ||
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| DifferentialExpressionComputeConfig computeConfig = getConfig(); | ||
| PluginUtil util = getUtil(); | ||
| ReferenceMetadata meta = getContext().getReferenceMetadata(); | ||
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| CollectionSpec collectionSpec = computeConfig.getCollectionVariable(); | ||
| CollectionDef collection = meta.getCollection(collectionSpec).orElseThrow(); | ||
| String collectionMemberType = collection.getMember() == null ? "unknown" : collection.getMember(); | ||
| String entityId = collectionSpec.getEntityId(); | ||
| EntityDef entity = meta.getEntity(entityId).orElseThrow(); | ||
| VariableDef computeEntityIdVarSpec = util.getEntityIdVarSpec(entityId); | ||
| String computeEntityIdColName = util.toColNameOrEmpty(computeEntityIdVarSpec); | ||
| String method = computeConfig.getDifferentialExpressionMethod().getValue().equals("DESeq") ? "DESeq" : "unknown"; | ||
| VariableSpec comparisonVariableSpec = computeConfig.getComparator().getVariable(); | ||
| String comparisonVariableDataShape = util.getVariableDataShape(comparisonVariableSpec); | ||
| List<LabeledRange> groupA = computeConfig.getComparator().getGroupA(); | ||
| List<LabeledRange> groupB = computeConfig.getComparator().getGroupB(); | ||
| String pValueFloor = computeConfig.getPValueFloor() != null ? computeConfig.getPValueFloor() : "1e-200"; // Same default as set in the frontend and microbiomeComputations | ||
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| // Get record id columns | ||
| List<VariableDef> idColumns = new ArrayList<>(); | ||
| for (EntityDef ancestor : meta.getAncestors(entity)) { | ||
| idColumns.add(ancestor.getIdColumnDef()); | ||
| } | ||
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| HashMap<String, InputStream> dataStream = new HashMap<>(); | ||
| dataStream.put(INPUT_DATA, getWorkspace().openStream(INPUT_DATA)); | ||
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| RServe.useRConnectionWithRemoteFiles(dataStream, connection -> { | ||
| connection.voidEval("print('starting differential expression computation')"); | ||
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| // Read in the count data | ||
| List<VariableSpec> computeInputVars = ListBuilder.asList(computeEntityIdVarSpec); | ||
| computeInputVars.addAll(util.getCollectionMembers(collectionSpec)); | ||
| computeInputVars.addAll(idColumns); | ||
| connection.voidEval(util.getVoidEvalFreadCommand(INPUT_DATA, computeInputVars)); | ||
| connection.voidEval("countData <- " + INPUT_DATA); // Renaming here so we can go get the sampleMetadata later | ||
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| // Read in the sample metadata | ||
| List<VariableSpec> sampleMetadataVars = ListBuilder.asList(comparisonVariableSpec); | ||
| sampleMetadataVars.add(computeEntityIdVarSpec); | ||
| connection.voidEval(util.getVoidEvalFreadCommand(INPUT_DATA, sampleMetadataVars)); | ||
| connection.voidEval("sampleMetadata <- veupathUtils::SampleMetadata(data = " + INPUT_DATA | ||
| + ", recordIdColumn = " + singleQuote(computeEntityIdColName) | ||
| + ")"); | ||
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| // Turn the list of id columns into an array of strings for R | ||
| List<String> dotNotatedIdColumns = idColumns.stream().map(VariableDef::toDotNotation).toList(); | ||
| StringBuilder dotNotatedIdColumnsString = new StringBuilder("c("); | ||
| boolean first = true; | ||
| for (String idCol : dotNotatedIdColumns) { | ||
| if (first) { | ||
| first = false; | ||
| dotNotatedIdColumnsString.append(singleQuote(idCol)); | ||
| } else { | ||
| dotNotatedIdColumnsString.append(",").append(singleQuote(idCol)); | ||
| } | ||
| } | ||
| dotNotatedIdColumnsString.append(")"); | ||
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| // Turn the comparator bin lists into a string for R | ||
| String rGroupA = util.getRBinListAsString(groupA); | ||
| String rGroupB = util.getRBinListAsString(groupB); | ||
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| // Create the comparator and input data objects | ||
| connection.voidEval("comparator <- veupathUtils::Comparator(" + | ||
| "variable=veupathUtils::VariableMetadata(" + | ||
| "variableSpec=veupathUtils::VariableSpec(" + | ||
| "variableId='" + comparisonVariableSpec.getVariableId() + "'," + | ||
| "entityId='" + comparisonVariableSpec.getEntityId() + "')," + | ||
| "dataShape = veupathUtils::DataShape(value = '" + comparisonVariableDataShape + "')" + | ||
| ")," + | ||
| "groupA=" + rGroupA + "," + | ||
| "groupB=" + rGroupB + | ||
| ")"); | ||
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| // TEMPORARY HACK FOR TESTING | ||
| // We dont have rnaseq data loaded yet (to my knowledge) so we are going to use mbio data and | ||
| // just convert it to counts. This is a hack and should be removed when we have real data | ||
| connection.voidEval("taxaColNames <- names(countData[, -c('" + computeEntityIdColName + "', as.character(" + dotNotatedIdColumnsString + "))])"); | ||
| connection.voidEval("countData[, (taxaColNames) := lapply(.SD,function(x) {round(x*1000)}), .SDcols=taxaColNames]"); | ||
| // END OF TEMP FOR TESTING | ||
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| connection.voidEval("countDataCollection <- veupathUtils::CountDataCollection(name=" + singleQuote(collectionMemberType) + | ||
| ", data=countData" + | ||
| ", sampleMetadata=sampleMetadata" + | ||
| ", recordIdColumn=" + singleQuote(computeEntityIdColName) + | ||
| ", ancestorIdColumns=as.character(" + dotNotatedIdColumnsString + ")" + | ||
| ", imputeZero=TRUE)"); | ||
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| connection.voidEval("computeResult <- veupathUtils::differentialExpression(" + | ||
| "collection=countDataCollection" + | ||
| ", comparator=comparator" + | ||
| ", method=" + singleQuote(method) + | ||
| ", pValueFloor=as.numeric(" + singleQuote(pValueFloor) + ")" + | ||
| ", verbose=TRUE)"); | ||
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| String statsCmd = "writeStatistics(computeResult, NULL, TRUE)"; | ||
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| getWorkspace().writeStatisticsResult(connection, statsCmd); | ||
| }); | ||
| } | ||
| } |
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