Support Rdiscvr SummarizeTCellActivation

singlecell/resources/chunks/SummarizeTCellActivation.R

@@ -0,0 +1,21 @@
+if (!file.exists('/homeDir/.netrc')) {
+    print(list.files('/homeDir'))
+    stop('Unable to find file: /homeDir/.netrc')
+}
+
+invisible(Rlabkey::labkey.setCurlOptions(NETRC_FILE = '/homeDir/.netrc'))
+Rdiscvr::SetLabKeyDefaults(baseUrl = serverBaseUrl, defaultFolder = defaultLabKeyFolder)
+
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    outFile <- paste0(outputPrefix, '.', makeLegalFileName(datasetId), '.activation.txt')
+    seuratObj <- Rdiscvr::SummarizeTNK_Activation(seuratObj, outFile = outFile, xFacetField = xFacetField, groupingFields = groupingFields, activationFieldName = activationFieldName, threshold = threshold)
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

singlecell/src/org/labkey/singlecell/SingleCellModule.java

@@ -220,6 +220,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new RunSDA.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunLDA.Provider());
         SequencePipelineService.get().registerPipelineStep(new FilterDisallowedClasses.Provider());
+        SequencePipelineService.get().registerPipelineStep(new SummarizeTCellActivation.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

singlecell/src/org/labkey/singlecell/pipeline/singlecell/SummarizeTCellActivation.java

@@ -0,0 +1,57 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.json.JSONObject;
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.Arrays;
+
+public class SummarizeTCellActivation extends AbstractRDiscvrStep
+{
+    public SummarizeTCellActivation(PipelineContext ctx, SummarizeTCellActivation.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("SummarizeTCellActivation", "Summarize TCell Activation", "RDiscvr", "This uses Rdiscvr::SummarizeTCellActivation to summarize cells with activation above a threshold.", Arrays.asList(
+                    SeuratToolParameter.create("groupingFields", "Grouping Field(s)", "The fields used to group cells.", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("allowBlank", false);
+                        put("height", 200);
+                        put("delimiter", ",");
+                        put("stripCharsRe", "/['\"]/g");
+                    }}, "SampleDate,Stim,Population,AssayType").delimiter(","),
+                    SeuratToolParameter.create("threshold", "Threshold", "Cells with a score greater than or equal to this are considered activated", "ldk-numberfield", new JSONObject(){{
+                        put("allowBlank", false);
+                        put("minValue", 0);
+                        put("maxValue", 1);
+                        put("decimalPrecision", 2);
+                    }}, 0.5),
+                    SeuratToolParameter.create("xFacetField", "X Facet Field", "A field used to facet the resulting plot", "textfield", new JSONObject(){{
+                        put("allowBlank", false);
+                    }}, "Population"),
+                    SeuratToolParameter.create("activationFieldName", "Activation Field Name", "The name of the field holding the score used to activation thresholding", "textfield", new JSONObject(){{
+                        put("allowBlank", false);
+                    }}, "TandNK_Activation_UCell")
+            ), null, null);
+        }
+
+        @Override
+        public SummarizeTCellActivation create(PipelineContext ctx)
+        {
+            return new SummarizeTCellActivation(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "activation";
+    }
+}
+