Support more options for celltypist

Author: bbimber

singlecell/resources/chunks/RunCelltypist.R

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

singlecell/resources/chunks/TrainCelltypist.R

@@ -6,4 +6,4 @@ datasetId <- names(seuratObjects)[[1]]
 printName(datasetId)
 seuratObj <- readRDS(seuratObjects[[datasetId]])
 
-RIRA::TrainCellTypist(seuratObj, labelField = labelField, minCellsPerClass = minCellsPerClass, modelFile = modelFile, tempFileLocation = '/work')
+RIRA::TrainCellTypist(seuratObj, labelField = labelField, minCellsPerClass = minCellsPerClass, excludedClasses = excludedClasses, modelFile = modelFile, tempFileLocation = '/work')

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

@@ -1,7 +1,9 @@
 package org.labkey.singlecell.pipeline.singlecell;
 
+import org.json.JSONObject;
 import org.labkey.api.sequenceanalysis.pipeline.AbstractPipelineStepProvider;
 import org.labkey.api.sequenceanalysis.pipeline.PipelineContext;
+import org.labkey.api.singlecell.pipeline.SeuratToolParameter;
 import org.labkey.api.singlecell.pipeline.SingleCellStep;
 
 import java.util.Arrays;
@@ -18,7 +20,26 @@ public static class Provider extends AbstractPipelineStepProvider<SingleCellStep
         public Provider()
         {
             super("RunCelltypist", "Run Celltypist (Built-In Model)", "Celltypist", "This will run Celltypist with the Immune_All_Low.pkl model.", Arrays.asList(
+                    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("columnPrefix", "Column Prefix", "If provided, this string will be added to the beginning of all output column names.", "textfield", new JSONObject()
+                    {{
 
+                    }}, null),
+                    SeuratToolParameter.create("pThreshold", "pThreshold", "This is passed to the --p-thres argument.", "ldk-numberfield", new JSONObject()
+                    {{
+                        put("minValue", 0);
+                        put("maxValue", 1);
+                        put("decimalPrecision", 3);
+                    }}, 0.5),
+                    SeuratToolParameter.create("minProp", "minProp", "This is passed to the --min-prop argument.", "ldk-numberfield", new JSONObject()
+                    {{
+                        put("minValue", 0);
+                        put("maxValue", 1);
+                        put("decimalPrecision", 3);
+                    }}, 0)
             ), null, null);
         }
 

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

@@ -48,7 +48,13 @@ public Provider()
                     SeuratToolParameter.create("minCellsPerClass", "Min Cells Per Class", "Any classes with fewer than this many cells will be dropped", "ldk-integerfield", new JSONObject()
                     {{
                         put("minValue", 0);
-                    }}, 100)
+                    }}, 100),
+                    SeuratToolParameter.create("excludedClasses", "Excluded Classes", "Any cells with these labels will be dropped. Note: NA can be used to drop NA values as well.", "textarea", new JSONObject()
+                    {{
+                        put("width", 400);
+                        put("height", 200);
+                        put("delimiter", ";");
+                    }}, "NA", "excludedClasses", true, true)
             ), null, null);
         }