dweemx
commented
3 years ago Hi @macsalvin,
You could use this R package https://github.com/aertslab/SCopeLoomR to add your embeddings (e.g.: in your case Seurat embedding) to the loom generated by the SCENIC protocol
Sorry for the late response
Hi, first of all thanks for this great tool.
I'm running the SCENIC protocol starting from the Seurat filtered object that was converted with loomR. Now I would like to see the results in Scope (http://scope.aertslab.org) in the seurat umap coordinates, is it possible to switch them?
After the last step "pyscenic aucell" I runned "python add_visualization.py" in order to visualize them in Scope and it was fine but I didn't find a way to change visualization from "SCENIC AUC UMAP" to Seurat umap. There is a way to change the default embedding?
Should I Integrate the data as specified in the integrated output in this notebook?
http://htmlpreview.github.io/?https://github.com/aertslab/SCENICprotocol/blob/master/notebooks/PBMC10k_SCENIC-protocol-CLI.html
Thanks again for this great tool.
Here the conversion from Seurat 3 to loom (umap information are converted into loom file):
Transposing input data: loom file will show input columns (cells) as rows and input rows (features) as columns This is to maintain compatibility with other loom tools |===================================================================================================================================================================================| 100% Adding: CellID Adding: Gene Adding a layer to norm_data (layer 1 of 1) |===================================================================================================================================================================================| 100% Adding: vst_mean Adding: vst_variance Adding: vst_variance_expected Adding: vst_variance_standardized Adding: vst_variable Adding: Selected Adding: orig_ident Adding: nCount_RNA Adding: nFeature_RNA Adding: Diagnosis Adding: Sample_Name Adding: Sample_Source Adding: Status Adding: percent_mt Adding: nCount_SCT Adding: nFeature_SCT Adding: seurat_clusters Adding: population Adding: celltype Adding: SCT_snn_res_2 Adding: CellType2 Adding: ClusterID Adding: ClusterName Adding scaled data matrix to /layers/scale_data Adding a layer to scale_data (layer 1 of 1) |===================================================================================================================================================================================| 100% Adding dimensional reduction information for pca Adding cell embedding information for pca Adding feature loading information for pca Adding dimensional reduction information for umap Adding cell embedding information for umap No feature loading information for umap Warning message: as.loom is being moved to SeuratDisk For more details, please see https://github.com/mojaveazure/seurat-disk/tree/feat/loom