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)
- 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 HOT 1
- Error in `Idents<-`: ! 'value' must be a factor or vector HOT 3
- Different results running. the same. code in different version. of HOT 6
- Protein complex HOT 1
- Function generate_info_tables return an error HOT 3
- Low AUPR values in analyses HOT 4
- RankActiveLigands Error
- Can NicheNet be used for analyzing three groups? HOT 1
- Parallelization error when optimizing parameters for NicheNet HOT 4
- How is the Ligand-Target-Matrix generated? HOT 2
- Receiver cells in differential analysis HOT 1
- when sender cell type is only one, HOT 1
- Only activating interactions or also repressing? HOT 1
- Naming convention in prioritization table
- Change error in `alias_to_symbol_seurat()` to warning
- discrepancy in results output HOT 2
- assign_ligands_to_celltype erroe message HOT 1
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