Add new param for ClrNormalizeByGroup

Author: bbimber

singlecell/resources/chunks/ClrNormalizeByGroup.R

@@ -1,7 +1,7 @@
 for (datasetId in names(seuratObjects)) {
     printName(datasetId)
     seuratObj <- readRDS(seuratObjects[[datasetId]])
-    seuratObj <- CellMembrane::ClrNormalizeByGroup(seuratObj, groupingVar = groupingVar, assayName = assayName, targetAssayName = targetAssayName, margin = margin, minCellsPerGroup = minCellsPerGroup, calculatePerFeatureUCell = calculatePerFeatureUCell, featureInclusionList = featureWhitelist, featureExclusionList = featureExclusionList)
+    seuratObj <- CellMembrane::ClrNormalizeByGroup(seuratObj, groupingVar = groupingVar, assayName = assayName, targetAssayName = targetAssayName, margin = margin, minCellsPerGroup = minCellsPerGroup, calculatePerFeatureUCell = calculatePerFeatureUCell, featureInclusionList = featureWhitelist, featureExclusionList = featureExclusionList, doAsinhTransform = doAsinhTransform)
 
     saveData(seuratObj, datasetId)
 

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

@@ -35,7 +35,10 @@ public Provider()
                     SeuratToolParameter.create("minCellsPerGroup", "Min Cells Per Group", "Any group with fewer than this many cells will be dropped.", "ldk-integerfield", new JSONObject(){{
 
                     }}, 20),
-                    SeuratToolParameter.create("calculatePerFeatureUCell", "Calculate Per Feature UCell ", "If checked, UCell will be run over each ", "checkbox", new JSONObject(){{
+                    SeuratToolParameter.create("calculatePerFeatureUCell", "Calculate Per Feature UCell ", "If checked, UCell will be run over each ADT", "checkbox", new JSONObject(){{
+                        put("checked", true);
+                    }}, true),
+                    SeuratToolParameter.create("doAsinhTransform", "Do asinh Transform ", "If checked, count data will be transformed using asinh prior to CLR", "checkbox", new JSONObject(){{
                         put("checked", 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(){{