Support PerformMhcDimRedux

BimberLab · Feb 19, 2025 · 869f213 · 869f213
1 parent 8193853
commit 869f213
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diff --git a/singlecell/resources/chunks/PerformMhcDimRedux.R b/singlecell/resources/chunks/PerformMhcDimRedux.R
@@ -0,0 +1,12 @@
+for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
+
+    seuratObj <- PerformMhcDimRedux(seuratObj)
+
+    saveData(seuratObj, datasetId)
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}
diff --git a/singlecell/src/org/labkey/singlecell/SingleCellModule.java b/singlecell/src/org/labkey/singlecell/SingleCellModule.java
@@ -72,6 +72,7 @@
 import org.labkey.singlecell.pipeline.singlecell.MergeSeurat;
 import org.labkey.singlecell.pipeline.singlecell.NormalizeAndScale;
 import org.labkey.singlecell.pipeline.singlecell.PerformDefaultNimbleAppend;
+import org.labkey.singlecell.pipeline.singlecell.PerformMhcDimRedux;
 import org.labkey.singlecell.pipeline.singlecell.PhenotypePlots;
 import org.labkey.singlecell.pipeline.singlecell.PlotAssayFeatures;
 import org.labkey.singlecell.pipeline.singlecell.PlotAverageCiteSeqCounts;
@@ -295,6 +296,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new UpdateSeuratPrototype.Provider());
         SequencePipelineService.get().registerPipelineStep(new RunDecoupler.Provider());
         SequencePipelineService.get().registerPipelineStep(new PerformDefaultNimbleAppend.Provider());
+        SequencePipelineService.get().registerPipelineStep(new PerformMhcDimRedux.Provider());
 
         SequenceAnalysisService.get().registerReadsetListener(new SingleCellReadsetListener());
     }

diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PerformMhcDimRedux.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/PerformMhcDimRedux.java
@@ -0,0 +1,38 @@
+package org.labkey.singlecell.pipeline.singlecell;
+
+import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
+import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SingleCellStep;
+
+import java.util.Arrays;
+
+public class PerformMhcDimRedux extends AbstractRDiscvrStep
+{
+    public PerformMhcDimRedux(PipelineContext ctx, PerformMhcDimRedux.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("PerformMhcDimRedux", "Perform MHC DimRedux", "RDiscvr", "This will perform dimensionality reduction based on MHC data", Arrays.asList(
+
+            ), null, null);
+        }
+
+        @Override
+        public PerformMhcDimRedux create(PipelineContext ctx)
+        {
+            return new PerformMhcDimRedux(ctx, this);
+        }
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "mhc";
+    }
+}
+