Support additional RIRA calling parameters

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

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

@@ -27,10 +27,6 @@ public Provider()
                         put("delimiter", ";");
                         put("joinReturnValue", true);
                     }}, "Immune_All_Low.pkl", null, true, true).delimiter(";"),
-                    SeuratToolParameter.create("convertAmbiguousToNA", "Convert Ambiguous To NA", "If true, any values for majority_voting with commas (indicating they are ambiguous) will be converted to NA", "checkbox", new JSONObject()
-                    {{
-                        put("checked", false);
-                    }}, false),
                     SeuratToolParameter.create("maxAllowableClasses", "Max Allowable Classes", "Celltypist can assign a cell to many classes, creating extremely long labels. Any cell with more than this number of labels will be set to NA", "ldk-integerfield", new JSONObject()
                     {{
                         put("minValue", 0);

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

@@ -34,10 +34,6 @@ public Provider()
                         put("performGenomeFilter", false);
                     }}, null),
                     SeuratToolParameter.create("columnPrefix", "Column Prefix", "This string will be pre-pended to the normal output columns (i.e. majority_voting and predicted_labels)", "textfield", null, null),
-                    SeuratToolParameter.create("convertAmbiguousToNA", "Convert Ambiguous To NA", "If true, any values for majority_voting with commas (indicating they are ambiguous) will be converted to NA", "checkbox", new JSONObject()
-                    {{
-                        put("checked", false);
-                    }}, false),
                     SeuratToolParameter.create("maxAllowableClasses", "Max Allowable Classes", "Celltypist can assign a cell to many classes, creating extremely long labels. Any cell with more than this number of labels will be set to NA", "ldk-integerfield", new JSONObject()
                     {{
                         put("minValue", 0);