gravatar for Pratik Mehta

2 hours ago by

University of Connecticut

How to embed known cell information into Seurat object? Using AddMetaData?

Is this possible?

I read this documentation: www.rdocumentation.org/packages/Seurat/versions/3.1.4/topics/AddMetaData

However I need some clarification on how to go about doing this, please?

I have cell labels that are all aligned with the expression matrix such as this:

"12wks_fetal pancreas cell_acinar"  "19wks_fetal pancreas cell_beta"    "12wks_fetal pancreas cell_ductal"  "12wks_fetal pancreas cell_beta"    "12wks_fetal pancreas cell_acinar"  "22wks_fetal pancreas cell_acinar"  "12wks_fetal pancreas cell_acinar"  "12wks_fetal pancreas cell_alpha"   "12wks_fetal pancreas cell_ductal"  "12wks_fetal pancreas cell_acinar"  "14wks_fetal pancreas cell_endocrine.progenitor..."

I used these cell labels as cell names (column names) for the expression matrix. However that's not useful for seeing which cell is from what time point 12wks, 19wks, 14 wks, etc. on the UMAP for example.

Would there be a way to label the cells using the AddMetaData function so that when I visualize the data using UMAP, they are color coded based on the time of collection (ie. 12wks, 19wks, 22wks, etc.) or would there be a way I could also filter by both time of collection and/or cell type?

Is this possible in Seurat? How would I approach this?

I would really appreciate anyone's help.

Very Respectfully,
Pratik

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Pratik Mehta10



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