generalize correlation plugins #87
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d-callan
changed the title
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so this still feels a bit hacky to me, but its way better than it was. i dont have the prefilters working yet, but im thinking that can be a separate pr, bc i want to think about how to best do that yet. also, i notice the values for member types are things like 'Host Eigengene' and i was expecting 'eigengene' regardless of host vs pathogen. i assume this is bc were also using these as display labels around places? if so, that makes me a bit uncomfortable that some fundamental logic here is based on completely free text strings as opposed to something w controlled values like at min an enum. |
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no the member should be 'eigengene'. I can start that change. |
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| if (isEigengene) { | ||
| connection.voidEval("assayData <- assayData[order(" + computeEntityIdColName + ")]; " + |
| String statsCmd = "writeStatistics(computeResult, NULL, TRUE)"; | ||
| if (isEigengene) { | ||
| connection.voidEval("abundanceData <- abundanceData[order(" + computeEntityIdColName + ")]; " + | ||
| "abundanceData <- abundanceData[, -as.character(" + dotNotatedIdColumnsString+ "), with=FALSE];" + |
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can we change this to 'assayData'? In the assaySelf version this naming distinction made it really clear what should be what.
| boolean isEigengene = false; | ||
| if (collection1MemberType.contains("Eigengene") || collection2MemberType.contains("Eigengene")) { | ||
| if (!(collection1MemberType.contains("Eigengene") && collection2MemberType.contains("Eigengene"))) { | ||
| throw new IllegalArgumentException("Both collection variables must have the same member type."); |
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Is this just for now? Generally this statement is not true.
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VEuPathDB/ApiCommonData@bee5e2c |
depends on VEuPathDB/veupathUtils#39
depends on VEuPathDB/microbiomeComputations#88
resolves #85