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aertslab / SCENIC

SCENIC is an R package to infer Gene Regulatory Networks and cell types from single-cell RNA-seq data.
http://scenic.aertslab.org
GNU General Public License v3.0
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How can we access Cell ID, tSNE Coordinates and Clustering metadata from SCENIC? #218

Closed AAA-3 closed 2 years ago

AAA-3 commented 2 years ago

Hello everyone!

I want to run RNA Velocity analysis and found this nice pipeline .

My SCENIC input was from Seurat, so I obtained the cell IDs from there already (I know SCopeLoom has get_cell_ids). SCENIC ran its own tSNE plots for which I would like to get the coordinates and clustering metadata for.

Any idea where/how I can locate this? SCopeLoom has get_clusterings_with_name and get_clusterings options but I do not know which one is most appropriate. And is there a way to do it without engaging with the .LOOM format?

In case it is relevant, this is for my binarized regulon tSNEs

par(mfrow=c(3,3))
fileNames <- paste0("int/",grep(".Rds", grep("tSNE_oHC_Binary", list.files("int"), value=T, perl = T), value=T))
plotTsne_compareSettings(fileNames, scenicOptions, varName="genotype", cex=.5)
AAA-3 commented 2 years ago

Figured it out i think!

tSNE_scenic[["Y"]]