Question: Adding UMAP coordinates to metadata
gravatar for roberts
5 days ago by
roberts0 wrote:

Hello, I want to store my umap coordinates in my seurat objects The umap coordinates are saved in my Object under reductions in cell.embeddings. How would I add this to the I tried running


I keep getting the error-- Error: Cannot add more or fewer cell information without values being named with cell names. Any suggestions? Thanks!

seurat R • 86 views
ADD COMMENTlink modified 5 days ago by fracarb850 • written 5 days ago by roberts0
gravatar for fracarb8
5 days ago by
fracarb850 wrote:

In Seurat 3, you can export the coordinates to a dataframe using Embeddings().

umapCoord <- = AD007[["umap"]]))

You can then add the PC columns to the as you please (cbind, sapply, paste(..,collapse=),...)

For example, if you only need to add the PCs components, without modifying them or doing other processing, you can do a simple merge

metadata_table <-
metadata_table$UMI_id <- rownames(metadata_table)
umapCoord$UMI_id <- rownames(umapCoord)
metadata_table <-,umapCoord,by = "UMI_id")
metadata_table$UMI_id <- NULL <- metadata_table

or if you want to be "seurat compliant"

AddMetaData(AD007, metadata=metadata_table)`

Always double check that the order of the cells between the metadata and the umap match.

ADD COMMENTlink modified 3 days ago • written 5 days ago by fracarb850

Thank you for your help. Just a follow up question how do I add PC to the (sorry I am new to coding). Thank you!

ADD REPLYlink written 4 days ago by roberts0

Check the edited answer

ADD REPLYlink written 3 days ago by fracarb850
Please log in to add an answer.


Use of this site constitutes acceptance of our User Agreement and Privacy Policy.
Powered by Biostar version 2.3.0
Traffic: 1783 users visited in the last hour