diff --git a/vignettes/integration_introduction.Rmd b/vignettes/integration_introduction.Rmd index bec4b4dd3..9ffc74639 100644 --- a/vignettes/integration_introduction.Rmd +++ b/vignettes/integration_introduction.Rmd @@ -139,7 +139,7 @@ We can explore these marker genes for each cluster and use them to annotate our ```{r annotate, results = 'hide', message=FALSE, fig.height = 8} FeaturePlot(immune.combined, features = c("CD3D", "SELL", "CREM", "CD8A", "GNLY", "CD79A", "FCGR3A", "CCL2", "PPBP"), min.cutoff = "q9") -immune.combined <- RenameIdents(immune.combined, "0" = "CD14 Mono", "1" = "CD4 Naive T", "2" = "CD4 Memory T", "3" = "CD16 Mono", "4" = "B", "5" = "CD8 T", "6" = "NK" , "7" = "T activated", "8" = "DC", "9" = "B Activated", "10" = "Mk", "11" = "pDC", "12" = "Eryth", "13" = "Mono/Mk Doublets", "14" = "HSPC") +immune.combined <- RenameIdents(immune.combined, "0" = "CD14 Mono", "1" = "CD4 Naive T", "2" = "CD4 Memory T", "3" = "CD16 Mono", "4" = "B", "5" = "CD8 T", "6" = "NK" , "7" = "T activated", "8" = "DC", "9" = "B Activated", "10" = "Mk", "11" = "pDC", "12" = "Eryth", "13" = "Mono/Mk Doublets") DimPlot(immune.combined, label = TRUE) ```