Support new RIRA RunScGateWithRhesusModels function

Author: bbimber

singlecell/resources/chunks/DropAssays.R

@@ -0,0 +1,14 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readRDS(seuratObjects[[datasetId]])
+
+    for (assayName in assayNames) {
+        if (assayName %in% names(seuratObj@assays)) {
+            seuratObj@assays[[assayName]] <- NULL
+        } else {
+            print(paste0('Assay not found, skipping: ', assayName))
+        }
+    }
+
+    saveData(seuratObj, datasetId)
+}

singlecell/resources/chunks/RunScGate.R

@@ -2,7 +2,11 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'), dropAmbiguousConsensusValues = dropAmbiguousConsensusValues, consensusModels = consensusModels)
+    if (useRhesusDefaults) {
+        seuratObj <- RIRA::RunScGateWithRhesusModels(seuratObj, dropAmbiguousConsensusValues = dropAmbiguousConsensusValues)
+    } else {
+        seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, labelRename = list(Tcell = 'T_NK', NK = 'T_NK'), dropAmbiguousConsensusValues = dropAmbiguousConsensusValues, consensusModels = consensusModels)
+    }
 
     saveData(seuratObj, datasetId)
 }

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

@@ -169,6 +169,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new CiteSeqWnn.Provider());
         SequencePipelineService.get().registerPipelineStep(new AvgExpression.Provider());
         SequencePipelineService.get().registerPipelineStep(new DimPlots.Provider());
+        SequencePipelineService.get().registerPipelineStep(new DropAssays.Provider());
         SequencePipelineService.get().registerPipelineStep(new FeaturePlots.Provider());
         SequencePipelineService.get().registerPipelineStep(new CiteSeqDimReduxPca.Provider());
         SequencePipelineService.get().registerPipelineStep(new CiteSeqPlots.Provider());

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

@@ -0,0 +1,37 @@
+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 DropAssays extends AbstractRiraStep
+{
+    public DropAssays(PipelineContext ctx, DropAssays.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("DropAssays", "Assay(s) to Drop", "Seurat", "This will drop the selected assays from your Seurat object(s)", Arrays.asList(
+                SeuratToolParameter.create("assayNames", "Assay(s)", "The names of assays to drop, such as: RNA.orig, ADT, or RNA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                            put("allowBlank", false);
+                            put("height", 150);
+                            put("delimiter", ",");
+                        }}, null).delimiter(",")
+                ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
+        }
+
+        @Override
+        public DropAssays create(PipelineContext ctx)
+        {
+            return new DropAssays(ctx, this);
+        }
+    }
+}

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

@@ -20,10 +20,12 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("RunScGate", "Run scGate", "scGate", "This will run scGate with the default built-in models and create a consensus call.", Arrays.asList(
+                    SeuratToolParameter.create("useRhesusDefaults", "Use Rhesus Default", "If checked, this will use the rhesus defaults, RIRA::RunScGateWithRhesusModels, and ignore the selections below", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true),
                     SeuratToolParameter.create("modelNames", "Model(s)", "The set of scGate modules to test.", "ldk-simplecombo", new JSONObject()
                     {{
                         put("multiSelect", true);
-                        put("allowBlank", false);
                         put("storeValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Erythrocyte;Epithelial;Platelet_MK");
                         put("initialValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Epithelial;Epithelial;Platelet_MK");
                         put("delimiter", ";");
@@ -32,7 +34,6 @@ public Provider()
                     SeuratToolParameter.create("consensusModels", "Models for Consensus", "The subset of models to be considered for the consensus call.", "ldk-simplecombo", new JSONObject()
                     {{
                         put("multiSelect", true);
-                        put("allowBlank", false);
                         put("storeValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Erythrocyte;Epithelial;Platelet_MK");
                         put("initialValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Epithelial");
                         put("delimiter", ";");
@@ -41,7 +42,7 @@ public Provider()
                     SeuratToolParameter.create("dropAmbiguousConsensusValues", "Drop Ambiguous Consensus Values", "If checked, any consensus calls that are ambiguous will be set to NA", "checkbox", new JSONObject(){{
                         put("checked", true);
                     }}, true)
-                    ), null, null);
+                ), null, null);
         }
 
         @Override