Expose celltypist batch size argument for large inputs

Author: bbimber

singlecell/resources/chunks/RunCelltypist.R

@@ -3,7 +3,7 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
     for (mn in modelNames) {
-        seuratObj <- RIRA::RunCellTypist(seuratObj, modelName = paste0(mn, '.pkl'), convertAmbiguousToNA = convertAmbiguousToNA, columnPrefix = paste0('celltypist.', mn, '.'), pThreshold = pThreshold, minProp = minProp, maxAllowableClasses = maxAllowableClasses, minFractionToInclude = minFractionToInclude, useMajorityVoting = useMajorityVoting, mode = mode)
+        seuratObj <- RIRA::RunCellTypist(seuratObj, modelName = paste0(mn, '.pkl'), convertAmbiguousToNA = convertAmbiguousToNA, columnPrefix = paste0('celltypist.', mn, '.'), pThreshold = pThreshold, minProp = minProp, maxAllowableClasses = maxAllowableClasses, minFractionToInclude = minFractionToInclude, useMajorityVoting = useMajorityVoting, mode = mode, maxBatchSize = maxBatchSize)
     }
 
     saveData(seuratObj, datasetId)

singlecell/resources/chunks/RunCelltypistCustomModel.R

@@ -2,7 +2,7 @@ for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-    seuratObj <- RIRA::RunCellTypist(seuratObj, modelName = modelFile, columnPrefix = columnPrefix, convertAmbiguousToNA = convertAmbiguousToNA, pThreshold = pThreshold, minProp = minProp, maxAllowableClasses = maxAllowableClasses, minFractionToInclude = minFractionToInclude, useMajorityVoting = useMajorityVoting, mode = mode)
+    seuratObj <- RIRA::RunCellTypist(seuratObj, modelName = modelFile, columnPrefix = columnPrefix, convertAmbiguousToNA = convertAmbiguousToNA, pThreshold = pThreshold, minProp = minProp, maxAllowableClasses = maxAllowableClasses, minFractionToInclude = minFractionToInclude, useMajorityVoting = useMajorityVoting, mode = mode, maxBatchSize = maxBatchSize)
 
     saveData(seuratObj, datasetId)
 }

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

@@ -62,7 +62,11 @@ public Provider()
                         put("minValue", 0);
                         put("maxValue", 1);
                         put("decimalPrecision", 3);
-                    }}, 0)
+                    }}, 0),
+                    SeuratToolParameter.create("maxBatchSize", "Max Cells Per Batch", "If the object has more than this many cells, celltypist will be run in batches", "ldk-integerfield", new JSONObject()
+                    {{
+                        put("minValue", 0);
+                    }}, 500000)
             ), null, null);
         }
 

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

@@ -69,7 +69,11 @@ public Provider()
                         put("minValue", 0);
                         put("maxValue", 1);
                         put("decimalPrecision", 3);
-                    }}, 0)
+                    }}, 0),
+                    SeuratToolParameter.create("maxBatchSize", "Max Cells Per Batch", "If the object has more than this many cells, celltypist will be run in batches", "ldk-integerfield", new JSONObject()
+                    {{
+                        put("minValue", 0);
+                    }}, 500000)
             ), PageFlowUtil.set("sequenceanalysis/field/SequenceOutputFileSelectorField.js"), null);
         }