Comments (1)
Thank you for your interest in our model.
The ligand_tf_matrix
is the output of the personalized page rank (PPR) algorithm. We used it to estimate signal propagation from ligands to transcription factors. In the original NicheNet paper, it is described as the ligand–gene signalling importance matrix.
To generate this matrix, we first joined the ligand-receptor network and the signalling network. Then, we ran the PPR to compute the probability of signal propagation from ligands to the other components of the signalling graph (such as the TFs). The output of the algorithm naturally displays the probability of transitioning to each node of the signalling graph, according to signal directionality. This explains the presence of probability scores from ligands to intermediate components of the signalling network, and not TFs only.
The ligand_target
matrix stores the regulatory potential scores, which is the product of the matrix multiplication between the previously described ligand–gene signalling importance matrix and the weighted adjacency matrix of the integrated gene regulatory network.
Please, refer to the original NicheNet paper for intuitive visualizations of the model. I omitted the details of the model optimization steps in my answer, but you can find all the details of the NicheNet V2 model in our MultiNicheNet preprint.
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Related Issues (20)
- How exactly the ligand activity were calculate? HOT 1
- I cannot run the "get_weighted_ligand_receptor_links" and "prepare_ligand_receptor_visualization" while I have nichnetr installed HOT 2
- Preferable metric to infer cell-to-cell communication HOT 1
- `get_exprs_avg` changes underscore to hyphen in cell type names
- How to choose the best ligand to continue analysis with the potential ligand?
- How should I assign a pathway/pathways to the target genes when running nichenetr? HOT 3
- cannot complete assign_ligands_to_celltype HOT 2
- missing function for circos plot visualization HOT 2
- I can't install nichenet HOT 1
- Condition_colname is not used for subsetting in nichenet_seuratobj_aggregate HOT 2
- `make_line_plot` bugs
- `assign_ligands_to_celltype` bug when there are no general ligands
- Error in `generate_info_tables`
- Warning message in `predict_ligand_activities`
- `generate_prioritization_tables` warnings and documentation
- Error when passing the recorrect_umi argument in get_lfc_celltype HOT 1
- Error in WhichCells.Seurat(object = object, idents = ident.2) : Cannot find the following identities in the object: Adjacent
- Error in `Idents<-`: ! 'value' must be a factor or vector
- Different results running. the same. code in different version. of HOT 1
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