Bugfix to re-running RIRA

bbimber · bbimber · commit dde9a8c34222 · 2026-06-08T14:28:02.000-07:00
diff --git a/singlecell/resources/chunks/UpdateSeuratPrototype.R b/singlecell/resources/chunks/UpdateSeuratPrototype.R
@@ -26,9 +26,9 @@ for (datasetId in names(seuratObjects)) {
   }
 
   if (runRira) {
-    seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, maxAllowedUnknown = maxAllowedUnknown)
-    seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
-    seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
+    seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE, maxAllowedUnknown = maxAllowedUnknown)
+    seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE)
+    seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE)
   }
 
   if (runTNKClassification) {

Original file line number	Diff line number	Diff line change
`@@ -26,9 +26,9 @@ for (datasetId in names(seuratObjects)) {`
`26`	`26`	`}`
`27`	`27`
`28`	`28`	`if (runRira) {`
`29`		`- seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, maxAllowedUnknown = maxAllowedUnknown)`
`30`		`- seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)`
`31`		`- seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)`
	`29`	`+ seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE, maxAllowedUnknown = maxAllowedUnknown)`
	`30`	`+ seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE)`
	`31`	`+ seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = 500000, retainProbabilityMatrix = FALSE)`
`32`	`32`	`}`
`33`	`33`
`34`	`34`	`if (runTNKClassification) {`