add differential expression #70
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| EntityDef entity = meta.getEntity(entityId).orElseThrow(); | ||
| VariableDef computeEntityIdVarSpec = util.getEntityIdVarSpec(entityId); | ||
| String computeEntityIdColName = util.toColNameOrEmpty(computeEntityIdVarSpec); | ||
| // if we ever introduce limma we can go back to this |
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Limma is another method for differential abundance analysis. But it's no longer on the horizon. Comment removed 👍
| VariableDef computeEntityIdVarSpec = util.getEntityIdVarSpec(entityId); | ||
| String computeEntityIdColName = util.toColNameOrEmpty(computeEntityIdVarSpec); | ||
| // if we ever introduce limma we can go back to this | ||
| String method = computeConfig.getDifferentialExpressionMethod().getValue().equals("DESeq") ? "DESeq" : "unknown"; |
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Should this throw an exception if it's not DESeq? There are no other options in the RAML.
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Yes, it does error if it doesn't receive DESeq. The api doesn't let it pass, but then also the R code will err as well if the method isn't DESeq.
| 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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Seems a bit roundabout loading as R variable differential_expression_input (aka INPUT_DATA) and then renaming immediately but I guess it's what we always do?
But, as you explain, we're reading the same file again into sampleMetadataVars so it makes sense.
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Yea I went back and forth on this a while, because you're right, it does seem a little roundabout. But I'm hoping it'll be a little faster this way!
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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("); |
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I think the following from our friend (assuming it works) might be more readable?
String dotNotatedIdColumnsString = "c(" +
dotNotatedIdColumns.stream()
.map(this::singleQuote)
.collect(Collectors.joining(",")) + ")";
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it didn't work, unfortunately, even with a little tweaking. Perhaps when my java skills are sharper i can revisit!
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No worries - sorry I didn't test it out myself!
| @Override | ||
| public PostAppsDifferentialexpressionVisualizationsVolcanoplotResponse postAppsDifferentialexpressionVisualizationsVolcanoplot(DifferentialExpressionVolcanoplotPostRequest entity) { | ||
| return wrapPlugin(() -> PostAppsDifferentialexpressionVisualizationsVolcanoplotResponse.respond200WithApplicationJson( | ||
| new DifferentialExpressionStatsResponseStream(processRequest(new DifferentialExpressionVolcanoplotPlugin(), entity)))); |
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I'm puzzling where DifferentialExpressionStatsResponseStream is defined...?
Is it in a previous PR?
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DifferentialExpressionStatsResponseStream gets automatically generated. The auto-generated files aren't usually tracked in git because there are too many of them. But it'll show up in eda/generated/model.
Adds a differential expression compute to the "compute service".
Fully functional. Test with VEuPathDB/veupathUtils#50
Can use
send to
computes/differentialexpression/For the volcanoplot, first ensure the above computation has finished, then send the following to
apps/differentialexpression/visualizations/volcanoplot