Question: Coloring cluster by cell type and parient id
gravatar for no
3 months ago by
no0 wrote:

Hello, I have been using Seurat for melanoma analysis. There are two tables I am using:

  1. An expression matrix where each row is a gene and each column is a cell
  2. A "cell_cluster_assignment" file where the cluster/cell type is given (for example: cell Cy72.... has cluster B, meaning it is a B cell)

Using the expression matrix, I can create a UMAP colored by principal components, but is there any way to color the UMAP using the "cell_cluster_assignment"?

umap rna-seq R • 129 views
ADD COMMENTlink written 3 months ago by no0


If I understood well, yes, it is possible you just need to provide an extra metadata column with the cluster information to Seurat. Assuming that the file cell_cluster_assignment contains a match between cell ids and cluster type, you can map the cluster type to Seurat metadata based on cell ids (the rownames of Seurat metadata table).

If you need more help, you need to provide a sample of your data and a code example. Otherwise it's difficult to help you.


ADD REPLYlink written 3 months ago by antonioggsousa1.5k
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