Support additional UCell/ssGSEA params

Author: bbimber

singlecell/resources/chunks/CustomUCell.R

@@ -20,6 +20,13 @@ for (datasetId in names(seuratObjects)) {
     print(Seurat::FeaturePlot(seuratObj, features = paste0(n, '_UCell'), min.cutoff = 'q02', max.cutoff = 'q98'))
   }
 
+  if (!is.null(outputAssayName)) {
+    dat <- as.matrix(seuratObj@meta.data[paste0(names(toCalculate), '_UCell')])
+    rownames(dat) <- rownames(seuratObj@meta.data)
+    colnames(dat) <- gsub(colnames(dat), pattern = '_', replacement = '-')
+    seuratObj[[outputAssayName]] <- Seurat::CreateAssayObject(data = Matrix::t(dat))
+  }
+
   saveData(seuratObj, datasetId)
 
   # Cleanup

singlecell/resources/chunks/RunEscape.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- CellMembrane::RunEscape(seuratObj, outputAssayName = outputAssayName, doPlot = TRUE)
+    seuratObj <- CellMembrane::RunEscape(seuratObj, outputAssayName = outputAssayName, doPlot = TRUE, performDimRedux = performDimRedux)
 
     saveData(seuratObj, datasetId)
 

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

@@ -37,7 +37,10 @@ public Provider()
                     }}, false, null, true),
                     SeuratToolParameter.create("assayName", "Assay Name", "Passed directly to UCell::AddModuleScore_UCell.", "textfield", new JSONObject(){{
 
-                    }}, "RNA")
+                    }}, "RNA"),
+                    SeuratToolParameter.create("outputAssayName", "Output Assay Name", "If provided, the set of UCell scores will be saved in a standalone assay.", "textfield", new JSONObject(){{
+
+                    }}, null, null, true)
             ), List.of("/sequenceanalysis/field/TrimmingTextArea.js"), null);
         }
 

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

@@ -23,7 +23,10 @@ public Provider()
             super("RunEscape", "Escape/ssGSEA", "escape", "Runs escape to perform ssGSEA using Hallmark gene sets.", Arrays.asList(
                     SeuratToolParameter.create("outputAssayName", "Output Assay Name", "The name of the assay to store results", "textfield", new JSONObject(){{
                         put("allowBank", false);
-                    }}, "escape.ssGSEA")
+                    }}, "escape.ssGSEA"),
+                    SeuratToolParameter.create("performDimRedux", "Perform DimRedux", "If true, the standard seurat PCA/FindClusters/UMAP process will be run on the escape data. This may be most useful when using a customGeneSet or a smaller set of features/pathways", "checkbox", new JSONObject(){{
+
+                    }}, false, null, true)
             ), null, null);
         }