Initial SDA support

Author: bbimber

singlecell/api-src/org/labkey/api/singlecell/pipeline/AbstractSingleCellPipelineStep.java

@@ -36,7 +36,7 @@ abstract public class AbstractSingleCellPipelineStep extends AbstractPipelineSte
 {
     public static final String SEURAT_THREADS = "seuratMaxThreads";
 
-    public AbstractSingleCellPipelineStep(PipelineStepProvider provider, PipelineContext ctx)
+    public AbstractSingleCellPipelineStep(PipelineStepProvider<?> provider, PipelineContext ctx)
     {
         super(provider, ctx);
     }
@@ -309,6 +309,11 @@ public static void executeR(SequenceOutputHandler.JobContext ctx, String dockerC
 
             if (seuratThreads != null)
             {
+                if (maxThreads != null && maxThreads < seuratThreads)
+                {
+                    seuratThreads = maxThreads;
+                }
+
                 writer.println("\t-e SEURAT_MAX_THREADS=" + seuratThreads + " \\");
             }
 

singlecell/resources/chunks/RunSDA.R

@@ -0,0 +1,20 @@
+if (Sys.getenv('SEURAT_MAX_THREADS') != '') {
+   nThreads <- Sys.getenv('SEURAT_MAX_THREADS')
+}
+
+ for (datasetId in names(seuratObjects)) {
+    printName(datasetId)
+    seuratObj <- readRDS(seuratObjects[[datasetId]])
+    gc()
+
+    outputFolder <- ''
+    if (dir.exists(outputFolder)) {
+       unlink(outputFolder, recursive = TRUE)
+    }
+
+    sdaResults <- bindArgs(CellMembrane::RunSDA, seuratObj)()
+
+    # Cleanup
+    rm(seuratObj)
+    gc()
+}

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

@@ -211,6 +211,7 @@ public static void registerPipelineSteps()
         SequencePipelineService.get().registerPipelineStep(new PlotAssayFeatures.Provider());
         SequencePipelineService.get().registerPipelineStep(new IntegrateData.Provider());
         SequencePipelineService.get().registerPipelineStep(new CustomUCell.Provider());
+        SequencePipelineService.get().registerPipelineStep(new RunSDA.Provider());
     }
 
     @Override

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

@@ -0,0 +1,73 @@
+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 RunSDA extends AbstractCellMembraneStep
+{
+    public RunSDA(PipelineContext ctx, RunSDA.Provider provider)
+    {
+        super(provider, ctx);
+    }
+
+    public static class Provider extends AbstractPipelineStepProvider<SingleCellStep>
+    {
+        public Provider()
+        {
+            super("RunSDA", "Run SDA", "CellMembrane/SDA", "This will run SDA on the seurat object.", Arrays.asList(
+                    SeuratToolParameter.create("numComps", "Num Comps", "Passed to SDAtools::run_SDA(). 30 is a good minimum but depends on input data complexity.", "ldk-integerfield", new JSONObject(){{
+                        put("minValue", 0);
+                    }}, 50),
+                    SeuratToolParameter.create("featureInclusionList", "Genes to Include", "These genes, entered comma-separated or one/line, will be added to the default Seurat::VariableFeatures gene set when running PCA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("height", 150);
+                        put("delimiter", ",");
+                        put("stripCharsRe", "/(^['\"]+)|(['\"]+$)/g");
+                    }}, null).delimiter(","),
+                    SeuratToolParameter.create("featureExclusionList", "Genes to Exclude", "These genes, entered comma-separated or one/line, will be excluded from the genes passed to RunPCA (which is otherwise determined by Seurat::VariableFeatures)", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("height", 150);
+                        put("delimiter", ",");
+                        put("stripCharsRe", "/(^['\"]+)|(['\"]+$)/g");
+                    }}, null).delimiter(","),
+                    SeuratToolParameter.create("minAsinhThreshold", "asinh Threshold", "This is used to filter genes. Only features with asinh(TOTAL_COUNTS) above this value are included.", "ldk-numberfield", new JSONObject(){{
+                        put("minValue", 0);
+                        put("decimalPrecision", 2);
+                    }}, 0.5, "minAsinhThreshold", false),
+                    SeuratToolParameter.create("minLibrarySize", "Min Library Size", "Passed to dropsim::normaliseDGE() min_library_size", "ldk-integerfield", new JSONObject(){{
+                        put("minValue", 0);
+                    }}, 50),
+                    SeuratToolParameter.create("max_iter", "Max Iterations", "Passed directly to SDAtools::run_SDA()", "ldk-integerfield", new JSONObject(){{
+                        put("minValue", 0);
+                    }}, 10000),
+                    SeuratToolParameter.create(SEURAT_THREADS, "Max Threads", "The number of threads to use. Cannot be higher than the threads allocated to the job.", "ldk-integerfield", new JSONObject(){{
+                        put("minValue", 0);
+                    }}, 8)
+                    ), Arrays.asList("/sequenceanalysis/field/TrimmingTextArea.js"), null);
+        }
+
+
+        @Override
+        public RunSDA create(PipelineContext ctx)
+        {
+            return new RunSDA(ctx, this);
+        }
+    }
+
+    @Override
+    public boolean createsSeuratObjects()
+    {
+        return false;
+    }
+
+    @Override
+    public String getFileSuffix()
+    {
+        return "sda";
+    }
+}
+
+