Add Phate t param

Author: bbimber

singlecell/resources/chunks/RunPHATE.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- CellMembrane::RunPHATE(seuratObj)
+    seuratObj <- CellMembrane::RunPHATE(seuratObj, t = ifelse(is.null(phateT), yes = 'auto', no = phateT))
     print(DimPlot(seuratObj, reduction = 'phate'))
 
     saveData(seuratObj, datasetId)

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

@@ -20,7 +20,7 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("RunPHATE", "Run PHATE", "CellMembrane/phateR", "This will run PHATE on the input object.", Arrays.asList(
-
+                SeuratToolParameter.create("phateT", "t", "Passed to the t parameter of phateR::phate().", "ldk-integerfield", null, null)
             ), null, null);
         }