Support cellhashing parameter to skip tSNE

Author: bbimber

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

@@ -106,6 +106,7 @@ public static class CellHashingParameters
         public Integer cells = 0;
         public boolean keepMarkdown = false;
         public File h5File = null;
+        public boolean doTSNE = true;
 
         private CellHashingParameters()
         {
@@ -120,6 +121,7 @@ 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.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);
             ret.htoReadset = htoReadset;
             ret.parentReadset = parentReadset;
@@ -160,6 +162,7 @@ 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.callerDisagreementThreshold = params.get("callerDisagreementThreshold") == null ? null : params.getDouble("callerDisagreementThreshold");
+            ret.doTSNE = params.get("doTSNE") == null ? true : params.getBoolean("doTSNE");
             ret.retainRawCountFile = params.optBoolean("retainRawCountFile", true);
             ret.htoReadset = htoReadset;
             ret.parentReadset = parentReadset;

singlecell/resources/views/singleCellDataManagement.html

@@ -64,7 +64,7 @@
                         url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_readsets', 'query.totalForwardReads~isnonblank': null, 'query.isArchived~eq': 0})
                     },{
                         name: 'Analyses Using Old Readsets',
-                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_analyses', 'query.readset/status~nonblank': null})
+                        url: LABKEY.ActionURL.buildURL('query', 'executeQuery.view', null, {schemaName: 'sequenceanalysis', queryName: 'sequence_analyses', 'query.readset/status~isnonblank': null})
                     }]
                 }]
             }]

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

@@ -897,10 +897,11 @@ public List<ToolParameterDescriptor> getHashingCallingParams(boolean allowDemuxE
                 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("retainRawCountFile", "Retain Raw Counts File", null, "checkbox", null, false)
         ));
 
-        final List<String> allMethods = Arrays.stream(CALLING_METHOD.values()).filter(x -> allowDemuxEm || x != CALLING_METHOD.demuxem).map(Enum::name).collect(Collectors.toList());
+        final List<String> allMethods = Arrays.stream(CALLING_METHOD.values()).filter(x -> allowDemuxEm || x != CALLING_METHOD.demuxem).map(Enum::name).toList();
         ret.add(ToolParameterDescriptor.create("methods", "Calling Methods", "The set of methods to use in calling.", "ldk-simplecombo", new JSONObject()
         {{
             put("multiSelect", true);
@@ -1188,9 +1189,10 @@ public File generateCellHashingCalls(File citeSeqCountOutDir, File outputDir, St
 
             String skipNormalizationQcString = parameters.skipNormalizationQc ? "TRUE" : "FALSE";
             String keepMarkdown = parameters.keepMarkdown ? "TRUE" : "FALSE";
+            String doTSNE = parameters.doTSNE ? "TRUE" : "FALSE";
             String h5String = h5 == null ? "" : ", h5File = '/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) + ")");
+            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("print('Rmarkdown complete')");
 
         }