Some warnings to look over (from student)

[rkhetani]

I have two warning messages although I could succeeded in following the homework.

-For “Clustering” part, when I run the following code, a warning message popped up. Even though I found this message, I succeeded in the following tasks. DimPlot(seurat_integrated,

• reduction = "umap",
• label = TRUE,
• label.size = 6) Warning message: Using as.character() on a quosure is deprecated as of rlang 0.3.0. Please use as_label() or as_name() instead. This warning is displayed once per session.

-For “Clustering quality control” part, when I run the following code, I found this warning. As I said earlier, I could see the same result as the textbook.

Determine metrics to plot present in seurat_integrated@meta.data

metrics <- c("nUMI", "nGene", "S.Score", "G2M.Score", "mitoRatio") FeaturePlot(seurat_integrated,

• reduction = "umap",
• features = metrics,
• pt.size = 0.4,
• sort.cell = TRUE,
• min.cutoff = 'q10',
• label = TRUE) Warning: The sort.cell parameter is being deprecated. Please use the order parameter instead for equivalent functionality.

[mistrm82]

updated all instances of this sort.cell argument to order. (cluster quality and marker identification lessons)