Label Clusters in Seurat

Question: Label Clusters in Seurat

11 months ago by

I have 2 plots, a control and stimulated group of cells.

After clustering, the cluster labels are 0, 1, 2.

EDIT How can I know what cell types are in each cluster? The known cell type names are in the rows of my data matrix, but how do I search for their names in the cluster?

>DimPlot(stem.combined, reduction = "umap", split.by = "control_subset")

Thanks

rna-seq seurat R • 2.6k views

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modified 11 months ago by Apoorva • 250 • written 11 months ago by planetearth • 0

11 months ago by

jared.andrews07 ♦ 6.2k

St. Louis, MO

jared.andrews07 ♦ 6.2k wrote:

This should do it.

# Save old identity classes (the cluster labels) for reference.
stem.combined[["old.ident"]] <- Idents(object = stem.combined)

# Rename classes.
stem.combined <- RenameIdents(object = stem.combined, `0` = "your cell type", `1` = "your other cell type", `2` = "your last cell type")

ADD COMMENT • link written 11 months ago by jared.andrews07 ♦ 6.2k

Thanks, but how would I know which cluster is which cell type? Is there a way to find the identity of my clusters?

ADD REPLY • link written 11 months ago by planetearth • 0

Oh, your original question made it sound like you already knew the types. You can look at the markers that best define each group via FindAllMarkers and use your expert knowledge of which cell types you expect to manually assign them. Or look at marker genes for various cell types that you expect just using FeaturePlot.

For an inference-based approach that uses reference expression profiles from dozens of different cell types, you can check out the R package SingleR. It is currently being prepped for Bioconductor submission and works quite well, particularly for immune cells. If you choose to use it, it's important to note the README is out of date. It should be installed via devtools::install_github("LTLA/SingleR").

ADD REPLY • link modified 11 months ago • written 11 months ago by jared.andrews07 ♦ 6.2k

11 months ago by

Apoorva • 250

United States

Apoorva • 250 wrote:

Another option is to use Garnett by the Trapnell lab, the same people who gave us monocle. It uses machine learning to train classifiers for a certain cell type and apply those classifiers to a single cell dataset

ADD COMMENT • link written 11 months ago by Apoorva • 250

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