Support minAllowableSingletRate in cell hashing

BimberLab · Jan 18, 2025 · 569af02 · 569af02
1 parent 806a1fb
commit 569af02
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Showing 2 changed files with 9 additions and 0 deletions.
diff --git a/singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java b/singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java
@@ -104,6 +104,7 @@ public static class CellHashingParameters
         public Integer minCountPerCell = 5;
         public Double majorityConsensusThreshold = null;
         public Double minAllowableDoubletRateFilter = null;
+        public Double minAllowableSingletRate = null;
         public Double callerDisagreementThreshold = null;
         public List<CALLING_METHOD> methods = CALLING_METHOD.getDefaultConsensusMethods(); //Default to just executing the set used for default consensus calls, rather than additional ones
         public List<CALLING_METHOD> consensusMethods = null;
@@ -127,6 +128,7 @@ public static CellHashingService.CellHashingParameters createFromStep(SequenceOu
             ret.minCountPerCell = step.getProvider().getParameterByName("minCountPerCell").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Integer.class, 3);
             ret.majorityConsensusThreshold = step.getProvider().getParameterByName("majorityConsensusThreshold").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null);
             ret.minAllowableDoubletRateFilter = step.getProvider().getParameterByName("minAllowableDoubletRateFilter").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null);
+            ret.minAllowableSingletRate = step.getProvider().getParameterByName("minAllowableSingletRate").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null);
             ret.callerDisagreementThreshold = step.getProvider().getParameterByName("callerDisagreementThreshold").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Double.class, null);
             ret.doTSNE = step.getProvider().getParameterByName("doTSNE").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false);
             ret.doNotAllowResume = step.getProvider().getParameterByName("doNotAllowResume").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false);
@@ -171,6 +173,7 @@ public static CellHashingParameters createFromJson(BARCODE_TYPE type, File webse
             ret.minCountPerCell = params.optInt("minCountPerCell", 3);
             ret.majorityConsensusThreshold = params.get("majorityConsensusThreshold") == null ? null : params.getDouble("majorityConsensusThreshold");
             ret.minAllowableDoubletRateFilter = params.get("minAllowableDoubletRateFilter") == null ? null : params.getDouble("minAllowableDoubletRateFilter");
+            ret.minAllowableSingletRate = params.get("minAllowableSingletRate") == null ? null : params.getDouble("minAllowableSingletRate");
             ret.callerDisagreementThreshold = params.get("callerDisagreementThreshold") == null ? null : params.getDouble("callerDisagreementThreshold");
             ret.doTSNE = params.optBoolean("doTSNE", false);
             ret.doNotAllowResume = params.optBoolean("doNotAllowResume", false);

diff --git a/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java b/singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java
@@ -979,6 +979,11 @@ public List<ToolParameterDescriptor> getHashingCallingParams(boolean allowMethod
                 put("maxValue", 1);
                 put("decimalPrecision", 2);
             }}, 0.2),
+                ToolParameterDescriptor.create("minAllowableSingletRate", "Min Allowable Singlet Rate", "This is an optional threshold designed to automatically discard poorly performing callers. If a given algorithm returns a singlet rate below this level, it is discarded from the consensus.", "ldk-numberfield", new JSONObject(){{
+                    put("minValue", 0);
+                    put("maxValue", 1);
+                    put("decimalPrecision", 2);
+                }}, 0.05),
             ToolParameterDescriptor.create("skipNormalizationQc", "Skip Normalization QC", null, "checkbox", null, true),
             ToolParameterDescriptor.create("doNotAllowResume", "Do Not Allow Resume", "If checked, on resume the job will repeat hashing scoring, rather than allowing resume from a saved state", "checkbox", null, false),
             ToolParameterDescriptor.create("doTSNE", "Do tSNE", "If true, tSNE will be performed as part of QC", "checkbox", null, false),
@@ -1275,6 +1280,7 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
                     ", majorityConsensusThreshold = " + (parameters.majorityConsensusThreshold == null ? "NULL" : parameters.majorityConsensusThreshold) +
                     ", callerDisagreementThreshold = " + (parameters.callerDisagreementThreshold == null ? "NULL" : parameters.callerDisagreementThreshold) +
                     (parameters.minAllowableDoubletRateFilter == null ? "" : ", minAllowableDoubletRateFilter = " + parameters.minAllowableDoubletRateFilter) +
+                    (parameters.minAllowableSingletRate == null ? "" : ", minAllowableSingletRate = " + parameters.minAllowableSingletRate) +
                     ", doTSNE = " + doTSNE + ")");
             writer.println("print('Rmarkdown complete')");