From 1d14cf4597f5a3630bd1d7188233d7c65acf53b1 Mon Sep 17 00:00:00 2001 From: simonmfr <70199914+simonmfr@users.noreply.github.com> Date: Thu, 16 Dec 2021 17:23:26 +0100 Subject: [PATCH] Update integration_introduction.Rmd Matched number of provided cell types to number of factor levels of immune.combined. Using 0:14 results in a warning: > 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") Warning: Cannot find identity 14 Reason: levels(Idents(immune.combined)) [1] "0" "1" "2" "3" "4" "5" "6" "7" "8" "9" "10" "11" "12" "13" --- vignettes/integration_introduction.Rmd | 2 +- 1 file changed, 1 insertion(+), 1 deletion(-) 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) ```