Support feature inclusion/exclusion lists for celltypist train

Author: bbimber

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, excludedClasses = excludedClasses, modelFile = modelFile, tempFileLocation = '/work')
+RIRA::TrainCellTypist(seuratObj, labelField = labelField, minCellsPerClass = minCellsPerClass, excludedClasses = excludedClasses, modelFile = modelFile, featureWhitelist = featureWhitelist, featureExclusionList = featureExclusionList, tempFileLocation = '/work')

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

@@ -54,7 +54,15 @@ public Provider()
                         put("width", 400);
                         put("height", 200);
                         put("delimiter", ";");
-                    }}, "NA", "excludedClasses", true, true)
+                    }}, "NA", "excludedClasses", true, true),
+                    SeuratToolParameter.create("featureWhitelist", "Genes to Add to VariableFeatures", "These genes, entered comma-separated or one/line, will be added to the default Seurat::VariableFeatures gene set when running PCA", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("height", 150);
+                        put("delimiter", ",");
+                    }}, null).delimiter(","),
+                    SeuratToolParameter.create("featureExclusionList", "Genes to Exclude From VariableFeatures", "These genes, entered comma-separated or one/line, will be excluded from the genes passed to RunPCA (which is otherwise determined by Seurat::VariableFeatures)", "sequenceanalysis-trimmingtextarea", new JSONObject(){{
+                        put("height", 150);
+                        put("delimiter", ",");
+                    }}, null).delimiter(",")
             ), null, null);
         }