Update seuratIntegrate.R

chenv3 · web-flow · commit 2c80868455dc · 2026-01-08T18:37:18.000-05:00
Fix bug for clustering results
diff --git a/workflow/scripts/seuratIntegrate.R b/workflow/scripts/seuratIntegrate.R
@@ -44,6 +44,7 @@ for (method in c('CCAIntegration', 'RPCAIntegration', 'HarmonyIntegration', 'Joi
     orig.reduction = "pca", new.reduction = reduction,
     verbose = FALSE
     )
+    obj <- FindNeighbors(obj, reduction = reduction, dims = 1:30)
     obj <- FindClusters(obj, resolution = 0.2, cluster.name = clusters)
     obj <- RunUMAP(obj, reduction = reduction, dims = 1:30, reduction.name = umap)
   })

Original file line number	Diff line number	Diff line change
`@@ -44,6 +44,7 @@ for (method in c('CCAIntegration', 'RPCAIntegration', 'HarmonyIntegration', 'Joi`
`44`	`44`	`orig.reduction = "pca", new.reduction = reduction,`
`45`	`45`	`verbose = FALSE`
`46`	`46`	`)`
	`47`	`+ obj <- FindNeighbors(obj, reduction = reduction, dims = 1:30)`
`47`	`48`	`obj <- FindClusters(obj, resolution = 0.2, cluster.name = clusters)`
`48`	`49`	`obj <- RunUMAP(obj, reduction = reduction, dims = 1:30, reduction.name = umap)`
`49`	`50`	`})`