explicitly set default correlation method for non-pass scatter plugins

VEuPathDB · May 7, 2024 · c3ba0f7 · c3ba0f7
1 parent 095295e
commit c3ba0f7
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Showing 4 changed files with 8 additions and 4 deletions.
diff --git a/...main/java/org/veupathdb/service/eda/data/plugin/abundance/AbundanceScatterplotPlugin.java b/...main/java/org/veupathdb/service/eda/data/plugin/abundance/AbundanceScatterplotPlugin.java
@@ -115,7 +115,7 @@ protected void writeResults(OutputStream out, Map<String, InputStream> dataStrea
       connection.voidEval("variables[[overlayVarIndex]] <- overlayVarMetadata");
 
       String command = "plot.data::scattergl(" + DEFAULT_SINGLE_STREAM_NAME + ", variables, '" +
-          valueSpec + "', NULL, TRUE, TRUE, '" + 
+          valueSpec + "', overlayValues=NULL, correlationMethod = 'none', sampleSizes=TRUE, completeCases=TRUE, '" + 
           deprecatedShowMissingness + "')";
       RServeClient.streamResult(connection, command, out);
     }); 

diff --git a/src/main/java/org/veupathdb/service/eda/data/plugin/alphadiv/AlphaDivScatterplotPlugin.java b/src/main/java/org/veupathdb/service/eda/data/plugin/alphadiv/AlphaDivScatterplotPlugin.java
@@ -127,7 +127,7 @@ protected void writeResults(OutputStream out, Map<String, InputStream> dataStrea
 
       String command = "plot.data::scattergl(" + DEFAULT_SINGLE_STREAM_NAME + ", variables, '" + 
                                                   valueSpec + 
-                                                  "', overlayValues=NULL, sampleSizes=TRUE, completeCases=TRUE, '" + 
+                                                  "', overlayValues=NULL, correlationMethod = 'none', sampleSizes=TRUE, completeCases=TRUE, '" + 
                                                   deprecatedShowMissingness + "')";
       RServeClient.streamResult(connection, command, out);
     }); 

diff --git a/src/main/java/org/veupathdb/service/eda/data/plugin/betadiv/BetaDivScatterplotPlugin.java b/src/main/java/org/veupathdb/service/eda/data/plugin/betadiv/BetaDivScatterplotPlugin.java
@@ -101,7 +101,10 @@ protected void writeResults(OutputStream out, Map<String, InputStream> dataStrea
       connection.voidEval(getVoidEvalComputedVariableMetadataList(metadata));
       connection.voidEval("variables <- veupathUtils::merge(variables, computedVariables)");
 
-      String command = "plot.data::scattergl(" + DEFAULT_SINGLE_STREAM_NAME + ", variables, '" + valueSpec + "', NULL, TRUE, TRUE, '" + deprecatedShowMissingness + "')";
+      String command = "plot.data::scattergl(" + DEFAULT_SINGLE_STREAM_NAME + ", variables, '" + 
+        valueSpec + 
+        "', overlayValues=NULL, correlationMethod = 'none', sampleSizes=TRUE, completeCases=TRUE, '" + 
+        deprecatedShowMissingness + "')";
       RServeClient.streamResult(connection, command, out);
     }); 
   }

diff --git a/...n/java/org/veupathdb/service/eda/data/plugin/standalonemap/FloatingScatterplotPlugin.java b/...n/java/org/veupathdb/service/eda/data/plugin/standalonemap/FloatingScatterplotPlugin.java
@@ -151,7 +151,8 @@ protected void writeResults(OutputStream out, Map<String, InputStream> dataStrea
       String cmd = 
           "plot.data::scattergl(data=" + inputData + ", " + 
                                   "variables=variables, " + 
-                                  "value='" + valueSpec + "', " + 
+                                  "value='" + valueSpec + "', " +
+                                  "correlationMethod = 'none', " +
                                   "sampleSizes=FALSE, " +
                                   "completeCases=FALSE, " + 
                                   "overlayValues=" + overlayValues + ", " +