DotPlot error in Seurat
0
0
Entering edit mode
14 months ago
synat.keam ▴ 100

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

enter image description here

#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()
Seurat single-cell • 533 views
ADD COMMENT

Login before adding your answer.

Traffic: 1676 users visited in the last hour
Help About
FAQ
Access RSS
API
Stats

Use of this site constitutes acceptance of our User Agreement and Privacy Policy.

Powered by the version 2.3.6