Seurat-to-RNA-Velocity icon indicating copy to clipboard operation
Seurat-to-RNA-Velocity copied to clipboard

Published 20 hours ago • verified publisher icon basilkhuder

Imported tSNE coordintes not being read!

Open AAA-3 opened this issue 3 years ago • 0 comments

I was wondering if anyone could help me here: I managed t oloadmy tsne coordinates but ran into an issue when I open the loom file and try to set the obsm_mapping parametre:

adata = scv.read_loom("/home/ali/Dokumente/RPractise/Velocity/PythonCodes/adata.loom", obs_names="CellID", var_names="Gene", obsm_mapping="X_tsne") image

Without setting the obsm_mapping parametre, the file loads normally and one can even see the tsne coordinates. Seeing as the information is available in the loom file, I assume that it is in an incorrect format...would it have something to do with it being an array? I notice that there is no ["tsne_1", "tsne_2"] headers, as listed in the scvelo.read_loom API page image

Anyone know how to resolve this?

AAA-3 avatar Aug 20 '21 09:08 AAA-3