Support minAllowableDoubletRateFilter

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/CellHashingService.java

@@ -103,14 +103,15 @@ public static class CellHashingParameters
         public boolean skipNormalizationQc = false;
         public Integer minCountPerCell = 5;
         public Double majorityConsensusThreshold = null;
+        public Double minAllowableDoubletRateFilter = 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;
         public String basename = null;
         public Integer cells = 0;
         public boolean keepMarkdown = false;
         public File h5File = null;
-        public boolean doTSNE = true;
+        public boolean doTSNE = false;
 
         private CellHashingParameters()
         {
@@ -124,6 +125,7 @@ public static CellHashingService.CellHashingParameters createFromStep(SequenceOu
             ret.skipNormalizationQc = step.getProvider().getParameterByName("skipNormalizationQc").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, false);
             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.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, null);
             ret.retainRawCountFile = step.getProvider().getParameterByName("retainRawCountFile").extractValue(ctx.getJob(), step.getProvider(), step.getStepIdx(), Boolean.class, true);
@@ -166,6 +168,7 @@ public static CellHashingParameters createFromJson(BARCODE_TYPE type, File webse
             ret.skipNormalizationQc = params.optBoolean("skipNormalizationQc", false);
             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.callerDisagreementThreshold = params.get("callerDisagreementThreshold") == null ? null : params.getDouble("callerDisagreementThreshold");
             ret.doTSNE = params.get("doTSNE") == null || params.getBoolean("doTSNE");
             ret.retainRawCountFile = params.optBoolean("retainRawCountFile", true);

singlecell/src/org/labkey/singlecell/CellHashingServiceImpl.java

@@ -964,8 +964,13 @@ public List<ToolParameterDescriptor> getHashingCallingParams(boolean allowMethod
                 put("maxValue", 1);
                 put("decimalPrecision", 2);
             }}, 0.2),
+            ToolParameterDescriptor.create("minAllowableDoubletRateFilter", "Min Allowable Doublet Rate Filter", "This applies to filtering algorithms based on their doublet rate. Typically, any algorithm with a high doublet rate (based on the theoretical rate) is discarded. This sets a minimum to the threshold used for triaging an algorithm", "ldk-numberfield", new JSONObject(){{
+                put("minValue", 0);
+                put("maxValue", 1);
+                put("decimalPrecision", 2);
+            }}, 0.2),
             ToolParameterDescriptor.create("skipNormalizationQc", "Skip Normalization QC", null, "checkbox", null, true),
-            ToolParameterDescriptor.create("doTSNE", "Do tSNE", "If true, tSNE will be performed as part of QC", "checkbox", null, true),
+            ToolParameterDescriptor.create("doTSNE", "Do tSNE", "If true, tSNE will be performed as part of QC", "checkbox", null, false),
             ToolParameterDescriptor.create("retainRawCountFile", "Retain Raw Counts File", null, "checkbox", null, false),
             ToolParameterDescriptor.create("failIfUnexpectedHtosFound", "Fail If Unexpected HTOs Found", "If checked and if there are any HTOs (testing all known HTOs) with counts above the HTOs expected in this experiment, then an error will be thrown", "checkbox", new JSONObject(){{
                 put("checked", true);
@@ -1263,7 +1268,21 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
             String doTSNE = parameters.doTSNE ? "TRUE" : "FALSE";
             String h5String = h5 == null ? "" : ", rawFeatureMatrixH5 = '/work/" + h5.getName() + "'";
             String consensusMethodString = consensusMethodNames.isEmpty() ? "" : ", methodsForConsensus = c('" + StringUtils.join(consensusMethodNames, "','") + "')";
-            writer.println("f <- cellhashR::CallAndGenerateReport(rawCountData = '/work/" + citeSeqCountOutDir.getName() + "'" + h5String + ", molInfoFile = '/work/" + molInfo.getName() + "', reportFile = '/work/" + htmlFile.getName() + "', callFile = '/work/" + callsFile.getName() + "', metricsFile = '/work/" + metricsFile.getName() + "', rawCountsExport = '/work/" + countFile.getName() + "', cellbarcodeWhitelist  = " + cellbarcodeWhitelist + ", barcodeWhitelist = " + allowableBarcodeParam + ", title = '" + parameters.getReportTitle() + "', skipNormalizationQc = " + skipNormalizationQcString + ", methods = c('" + StringUtils.join(methodNames, "','") + "')" + consensusMethodString + ", keepMarkdown = " + keepMarkdown + ", minCountPerCell = " + (parameters.minCountPerCell == null ? "NULL" : parameters.minCountPerCell) + ", majorityConsensusThreshold = " + (parameters.majorityConsensusThreshold == null ? "NULL" : parameters.majorityConsensusThreshold) + ", callerDisagreementThreshold = " + (parameters.callerDisagreementThreshold == null ? "NULL" : parameters.callerDisagreementThreshold) + ", doTSNE = " + doTSNE + ")");
+            writer.println("f <- cellhashR::CallAndGenerateReport(rawCountData = '/work/" + citeSeqCountOutDir.getName() + "'" + h5String + ", molInfoFile = '/work/" + molInfo.getName() +
+                    "', reportFile = '/work/" + htmlFile.getName() +
+                    "', callFile = '/work/" + callsFile.getName() +
+                    "', metricsFile = '/work/" + metricsFile.getName() +
+                    "', rawCountsExport = '/work/" + countFile.getName() +
+                    "', cellbarcodeWhitelist  = " + cellbarcodeWhitelist + ", barcodeWhitelist = " + allowableBarcodeParam +
+                    ", title = '" + parameters.getReportTitle() +
+                    "', skipNormalizationQc = " + skipNormalizationQcString +
+                    ", methods = c('" + StringUtils.join(methodNames, "','") + "')" + consensusMethodString +
+                    ", keepMarkdown = " + keepMarkdown +
+                    ", minCountPerCell = " + (parameters.minCountPerCell == null ? "NULL" : parameters.minCountPerCell) +
+                    ", majorityConsensusThreshold = " + (parameters.majorityConsensusThreshold == null ? "NULL" : parameters.majorityConsensusThreshold) +
+                    ", callerDisagreementThreshold = " + (parameters.callerDisagreementThreshold == null ? "NULL" : parameters.callerDisagreementThreshold) +
+                    (parameters.minAllowableDoubletRateFilter == null ? "" : "', minAllowableDoubletRateFilter = " + parameters.minAllowableDoubletRateFilter) +
+                    ", doTSNE = " + doTSNE + ")");
             writer.println("print('Rmarkdown complete')");
 
         }