Add line to ensure non-T/NK cells are not classified as t/nk subsets

bbimber · bbimber · commit cba0d2cf9787 · 2023-01-04T15:20:22.000-08:00
diff --git a/singlecell/resources/chunks/RunRiraClassification.R b/singlecell/resources/chunks/RunRiraClassification.R
@@ -3,7 +3,9 @@ for (datasetId in names(seuratObjects)) {
     seuratObj <- readRDS(seuratObjects[[datasetId]])
 
     seuratObj <- RIRA::RunCellTypist(seuratObj, modelName = 'RIRA_Immune_v1', maxBatchSize = maxBatchSize, columnPrefix = 'RIRA_Immune_v1.', retainProbabilityMatrix = retainProbabilityMatrix)
-    seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
+    seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, columnPrefix = 'RIRA_TNK_v2.')
+
+    seuratObj$RIRA_TNK_v2.predicted_labels[seuratObj$RIRA_Immune_v1.majority_voting != 'T_NK'] <- 'Other'
 
     saveData(seuratObj, datasetId)
 }

Original file line number	Diff line number	Diff line change
`@@ -3,7 +3,9 @@ for (datasetId in names(seuratObjects)) {`
`3`	`3`	`seuratObj <- readRDS(seuratObjects[[datasetId]])`
`4`	`4`
`5`	`5`	`seuratObj <- RIRA::RunCellTypist(seuratObj, modelName = 'RIRA_Immune_v1', maxBatchSize = maxBatchSize, columnPrefix = 'RIRA_Immune_v1.', retainProbabilityMatrix = retainProbabilityMatrix)`
`6`		`- seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)`
	`6`	`+ seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix, columnPrefix = 'RIRA_TNK_v2.')`
	`7`	`+`
	`8`	`+ seuratObj$RIRA_TNK_v2.predicted_labels[seuratObj$RIRA_Immune_v1.majority_voting != 'T_NK'] <- 'Other'`
`7`	`9`
`8`	`10`	`saveData(seuratObj, datasetId)`
`9`	`11`	`}`