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cliffren / PENCIL

PENCIL is a novel tool for singlecell data analysis to identify phenotype associated subpopulations and informative genes simultaneously.
GNU General Public License v3.0
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UMAP inconsistencies in R tutorials #2

Closed cliffren closed 1 year ago

cliffren commented 1 year ago

In the R tutorial, the graphs generated from umap coordinates and umap-mvg2000 coordinates are the same.

cliffren commented 1 year ago

This doesn't appear when using seurat 4.1.1, but appears in higher versions such as 4.3 due to naming conflicts. Thanks to Famingzhao for a solution. 

sc_data[["umap"]] <- CreateDimReducObject(embeddings = as.matrix(sc_data@reductions$umap@cell.embeddings), key = "UMAPRaw", assay = "RNA")