Support new gene component

Author: bbimber

singlecell/resources/chunks/CalculateGeneComponentScores.R

@@ -10,7 +10,7 @@ for (datasetId in names(seuratObjects)) {
 
     for (sc in savedComponent) {
         logger::log_info(paste0('Processing ', datasetId, ' for ', sc))
-        seuratObj <- RIRA::ScoreUsingSavedComponent(seuratObj, componentOrName = sc, fieldName = sc)
+        seuratObj <- RIRA::ScoreUsingSavedComponent(seuratObj, componentOrName = sc, fieldName = sc, layer = ifelse(useScaledData, yes = 'scale.data', no = 'data'))
     }
 
     saveData(seuratObj, datasetId)

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

@@ -7,8 +7,8 @@
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 import org.labkey.api.util.PageFlowUtil;
 
+import java.util.Arrays;
 import java.util.Collection;
-import java.util.Collections;
 
 public class CalculateGeneComponentScores extends AbstractRiraStep
 {
@@ -21,16 +21,16 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
     {
         public Provider()
         {
-            super("CalculateGeneComponentScores", "Calculate Gene Module Scores", "RIRA", "This will generate UCell scores for a set of pre-defined gene modules", Collections.singletonList(
+            super("CalculateGeneComponentScores", "Calculate Gene Module Scores", "RIRA", "This will generate UCell scores for a set of pre-defined gene modules", Arrays.asList(
                     SeuratToolParameter.create("savedComponent", "Saved Component(s)", "This is the name of the saved component (from RIRA) to apply", "ldk-simplecombo", new JSONObject()
                     {{
-                        put("storeValues", "Tcell_EffectorDifferentiation;TCR_EarlyStimulationComponent;CD4_Activation_Axis");
+                        put("storeValues", "Tcell_EffectorDifferentiation;TCR_EarlyStimulationComponent;CD4_Activation_Axis;PRF1_EffectorAxis");
                         put("multiSelect", true);
                         put("allowBlank", false);
                         put("joinReturnValue", true);
                         put("delimiter", ";");
-
-                    }}, "Tcell_EffectorDifferentiation", null, true, true).delimiter(";")
+                    }}, "Tcell_EffectorDifferentiation", null, true, true).delimiter(";"),
+                    SeuratToolParameter.create("useScaledData", "Use scale.data", "By default, these are calculated against the data slot. If checked, it will use scale.data instead", "checkbox", null, false)
             ), null, null);
         }