fix from bcbior #138

bcbio/bcbioR#138
cc @eberdan

Author: lpantano

02_integration/norm_integration.rmd

@@ -336,6 +336,9 @@ seurat_sctnorm <- SCTransform(seurat_lognorm,
   # vars.to.regress = c("mitoRatio")
   variable.features.n = 3000
 )
+seurat_sctnorm <- RunPCA(seurat_sctnorm)
+seurat_sctnorm <- RunUMAP(seurat_sctnorm, 1:40)
+
 saveRDS(seurat_sctnorm, file = "seurat_sctnorm.rds")
 ```
 
@@ -347,7 +350,6 @@ We qualitatively reviewed the "structure" in our normalized data projection . We
 
 ```{r, fig.width=10}
 DefaultAssay(seurat_sctnorm) <- "SCT"
-seurat_sctnorm <- RunPCA(seurat_sctnorm)
 UMAPPlot(seurat_sctnorm, group.by = "orig.ident") + ggtitle("UMAP")
 ```