Support maxLibrarySizeRatio for nimble

BimberLab · Jan 10, 2024 · fa471aa · fa471aa
1 parent 98cfa80
commit fa471aa
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Showing 2 changed files with 6 additions and 2 deletions.
diff --git a/singlecell/resources/chunks/AppendNimble.R b/singlecell/resources/chunks/AppendNimble.R
@@ -11,7 +11,7 @@ for (datasetId in names(seuratObjects)) {
   seuratObj <- readSeuratRDS(seuratObjects[[datasetId]])
 
   for (genomeId in names(nimbleGenomes)) {
-    seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE, dropAmbiguousFeatures = !retainAmbiguousFeatures)
+    seuratObj <- Rdiscvr::DownloadAndAppendNimble(seuratObject = seuratObj, allowableGenomes = genomeId, targetAssayName = nimbleGenomes[[genomeId]], enforceUniqueFeatureNames = TRUE, dropAmbiguousFeatures = !retainAmbiguousFeatures, maxLibrarySizeRatio = maxLibrarySizeRatio)
   }
 
   saveData(seuratObj, datasetId)

diff --git a/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendNimble.java b/singlecell/src/org/labkey/singlecell/pipeline/singlecell/AppendNimble.java
@@ -35,7 +35,11 @@ public Provider()
                     SeuratToolParameter.create("retainAmbiguousFeatures", "Retain Ambiguous Features", "If checked, features hitting more than one reference will be retained", "checkbox", new JSONObject()
                     {{
                         put("check", false);
-                    }}, false, null, true)
+                    }}, false, null, true),
+                    SeuratToolParameter.create("maxLibrarySizeRatio", "Max Library Size Ratio", "This normalization relies on the assumption that the library size of the assay being normalized in negligible relative to the assayForLibrarySize. To verify this holds true, the method will error if librarySize(assayToNormalize)/librarySize(assayForLibrarySize) exceeds this value", "ldk-numberfield", new JSONObject()
+                    {{
+                        put("decimalPrecision", 4);
+                    }}, 0.1, null, true)
             ), Arrays.asList("sequenceanalysis/field/GenomeField.js", "/singlecell/panel/NimbleAppendPanel.js"), null);
         }