Support more celltypist params

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)
+        seuratObj <- RIRA::RunCellTypist(seuratObj, modelName = paste0(mn, '.pkl'), convertAmbiguousToNA = convertAmbiguousToNA, columnPrefix = paste0('celltypist.', mn, '.'), pThreshold = pThreshold, minProp = minProp, maxAllowableClasses = maxAllowableClasses, minFractionToInclude = minFractionToInclude)
     }
 
     saveData(seuratObj, datasetId)

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

@@ -33,6 +33,12 @@ public Provider()
                     {{
                         put("minValue", 0);
                     }}, 5),
+                    SeuratToolParameter.create("minFractionToInclude", "Min Fraction To Include", "Any labels representing fewer than this fraction of the cells will be set to NA", "ldk-numberfield", new JSONObject()
+                    {{
+                        put("minValue", 0);
+                        put("maxValue", 1);
+                        put("decimalPrecision", 3);
+                    }}, 0.01),
                     SeuratToolParameter.create("pThreshold", "pThreshold", "This is passed to the --p-thres argument.", "ldk-numberfield", new JSONObject()
                     {{
                         put("minValue", 0);