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Add effect direction to volcano plot output filter #18

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Add effect direction to volcano plot output filter #18

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24 changes: 22 additions & 2 deletions WSFPlugin/src/main/java/org/apidb/apicomplexa/wsfplugin/eda/GeneEdaVizWithComputePlugin.java
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Original file line number Diff line number Diff line change
Expand Up @@ -36,6 +36,18 @@ public class GeneEdaVizWithComputePlugin extends AbstractEdaGenesPlugin {

private static final Logger LOG = Logger.getLogger(GeneEdaVizWithComputePlugin.class);

private enum EffectDirection {
UP_AND_DOWN, UP_ONLY, DOWN_ONLY;

static EffectDirection fromString(String s) {
return switch (s == null ? "" : s) {
case "up only" -> UP_ONLY;
case "down only" -> DOWN_ONLY;
default -> UP_AND_DOWN;
};
}
}

private static class Point {

String pointId;
Expand All @@ -52,6 +64,7 @@ public String toString() {

private double _effectSizeThreshold;
private double _significanceThreshold;
private EffectDirection _effectDirection;
private Path _tmpFile;

@Override
Expand Down Expand Up @@ -135,6 +148,7 @@ protected InputStream getEdaTabularDataStream(String edaBaseUrl, Map<String, Str
// values to be used later to filter returned rows
_effectSizeThreshold = vizConfig.getDouble("effectSizeThreshold");
_significanceThreshold = vizConfig.getDouble("significanceThreshold");
_effectDirection = EffectDirection.fromString(vizConfig.optString("effectDirection", "up and down"));

// make request with JSON like
/**
Expand Down Expand Up @@ -383,9 +397,15 @@ private void handleComputeStatus(String edaBaseUrl, String studyId, JSONArray fi
protected Boolean isRetainedRow(String[] edaRow) {
try {
//LOG.info("Checking if edaRow of size " + edaRow.length + " should be retained, array = [ " + String.join(", ", edaRow) + " ]");
double effectSize = Math.abs(Double.valueOf(edaRow[1]));
double rawEffectSize = Double.valueOf(edaRow[1]);
double effectSize = Math.abs(rawEffectSize);
double pValue = Math.abs(Double.valueOf(edaRow[2]));
return pValue <= _significanceThreshold && effectSize >= _effectSizeThreshold;
if (!(pValue <= _significanceThreshold && effectSize >= _effectSizeThreshold)) return false;
return switch (_effectDirection) {
case UP_ONLY -> rawEffectSize > 0;
case DOWN_ONLY -> rawEffectSize < 0;
default -> true;
};
}
catch (NumberFormatException e) {
LOG.warn("Skipping EDA output row in which effectSize or pValue property is not a valid double value. Row = [ " + String.join(", ", edaRow) + " ]", e);
Expand Down