Split RunScGate step to make less confusing

Author: bbimber

singlecell/resources/chunks/RunScGate.R

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

singlecell/resources/chunks/RunScGateBuiltin.R

@@ -0,0 +1,8 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- RIRA::RunScGateForModels(seuratObj, modelNames = modelNames, dropAmbiguousConsensusValues = dropAmbiguousConsensusValues, consensusModels = consensusModels, assay = assayName)
+
+    saveData(seuratObj, datasetId)
+}

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

@@ -199,6 +199,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new PlotAverageCiteSeqCounts.Provider());
         SequencePipelineService.get().registerPipelineStep(new DropCiteSeq.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunScGate.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunScGateBuiltin.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunCelltypist.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunCelltypistCustomModel.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunRiraClassification.Provider());

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

@@ -19,26 +19,7 @@ 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("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", ";");
-                        put("joinReturnValue", true);
-                    }}, null, null, true, true),
-                    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("storeValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Erythrocyte;Epithelial;Platelet_MK");
-                        put("initialValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Epithelial");
-                        put("delimiter", ";");
-                        put("joinReturnValue", true);
-                    }}, null, null, true, true),
+            super("RunScGate", "Run scGate", "scGate", "This will run scGate with the default rhesus RIRA models and create a consensus call.", Arrays.asList(
                     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),

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

@@ -0,0 +1,54 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.json.old.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 RunScGateBuiltin extends AbstractRiraStep
+{
+    public RunScGateBuiltin(PipelineContext ctx, RunScGateBuiltin.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunScGateBuildin", "Run scGate (built-in)", "scGate", "This will run scGate with the default built-in models and create a consensus call.", Arrays.asList(
+                    SeuratToolParameter.create("modelNames", "Model(s)", "The set of scGate modules to test.", "ldk-simplecombo", new JSONObject()
+                    {{
+                        put("multiSelect", true);
+                        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", ";");
+                        put("joinReturnValue", true);
+                    }}, null, null, true, true),
+                    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("storeValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Erythrocyte;Epithelial;Platelet_MK");
+                        put("initialValues", "Bcell;Tcell;NK;Myeloid;Stromal;pDC;Epithelial");
+                        put("delimiter", ";");
+                        put("joinReturnValue", true);
+                    }}, null, null, true, true),
+                    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),
+                    SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "textfield", new JSONObject(){{
+
+                    }}, "RNA")
+                ), null, null);
+        }
+
+        @Override
+        public RunScGateBuiltin create(PipelineContext ctx)
+        {
+            return new RunScGateBuiltin(ctx, this);
+        }
+    }
+}