Add Classify_Myeloid to RIRA step

bbimber · bbimber · commit 5587aec4fb97 · 2024-06-07T10:42:23.000-07:00
diff --git a/singlecell/resources/chunks/RunRiraClassification.R b/singlecell/resources/chunks/RunRiraClassification.R
@@ -4,8 +4,9 @@ for (datasetId in names(seuratObjects)) {
 
     seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
     seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
-
     seuratObj$RIRA_TNK_v2.predicted_labels[seuratObj$RIRA_Immune_v2.majority_voting != 'T_NK'] <- 'Other'
 
+    seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)
+
     saveData(seuratObj, datasetId)
 }

Original file line number	Diff line number	Diff line change
`@@ -4,8 +4,9 @@ for (datasetId in names(seuratObjects)) {`
`4`	`4`
`5`	`5`	`seuratObj <- RIRA::Classify_ImmuneCells(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)`
`6`	`6`	`seuratObj <- RIRA::Classify_TNK(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)`
`7`		`-`
`8`	`7`	`seuratObj$RIRA_TNK_v2.predicted_labels[seuratObj$RIRA_Immune_v2.majority_voting != 'T_NK'] <- 'Other'`
`9`	`8`
	`9`	`+ seuratObj <- RIRA::Classify_Myeloid(seuratObj, maxBatchSize = maxBatchSize, retainProbabilityMatrix = retainProbabilityMatrix)`
	`10`	`+`
`10`	`11`	`saveData(seuratObj, datasetId)`
`11`	`12`	`}`