Dear All,

Sorry for another question. I have seurat integrated object, which was annotated with cell types and have three conditions with 3 sample per condition. I would like to replicate some codes in seurat, but was error Error: None of the provided identity class levels were found and not sure how to fix. type variable has three group in there and I would like to visualize cell type of three groups in dotplot. I have attached Seurat graph for reference, but in Seurat example, there was only two groups. hope you could help fix.

Kind Regards

#view metadata
view(Athritis_annotation)

#mach identity 
Idents(Athritis_annotation) <- factor(Idents(Athritis_annotation), levels = c("CD4", "CD8", "Naive CD4",
                                            "CD8 effector/memo", "Gamma/delta T", "Treg", 
                                           "Proliferating T", "NK & NK T", "B cell"))

## define markers
markers.to.plot <- c("CD3E","CD3D", "CD4", "CD8A", "FOXP3", "CCR7", "CD69", "CXCR3", "CXCR5", "CXCR6", "CCR4", "CCR6", "KLRB1", "IL2RA", "IL7R", "KLRG1", "CXCL13", "TOX", "LAG3", "CTLA4", "PDCD1", "HAVCR2", "TIGIT", "EOMES", "CX3CR1", "MKI67", "TRGV9", 
              "TRGV2", "FCGR3A", "NCAM1")

#visualization plot 
DotPlot(Athritis_annotation, features = rev(markers.to.plot), cols = c("blue", "red", "green"), dot.scale = 8, 
    split.by = "type") + RotatedAxis()