View source: R/application_prediction.R
normalize_single_cell_ligand_activities | R Documentation |
normalize_single_cell_ligand_activities
Normalize single-cell ligand activities to make ligand activities over different cells comparable.
normalize_single_cell_ligand_activities(ligand_activities)
ligand_activities |
Output from the function 'predict_single_cell_ligand_activities'. |
A tibble giving the normalized ligand activity scores for single cells. Following columns in the tibble: $cell, $ligand, $pearson, which is the normalized ligand activity value.
## Not run:
weighted_networks = construct_weighted_networks(lr_network, sig_network, gr_network,source_weights_df)
ligands = list("TNF","BMP2","IL4")
ligand_target_matrix = construct_ligand_target_matrix(weighted_networks, ligands, ltf_cutoff = 0, algorithm = "PPR", damping_factor = 0.5, secondary_targets = FALSE)
potential_ligands = c("TNF","BMP2","IL4")
genes = c("SOCS2","SOCS3","IRF1","ICAM1","ID1","ID2","ID3")
cell_ids = c("cell1","cell2")
expression_scaled = matrix(rnorm(length(genes)*2, sd = 0.5, mean = 0.5), nrow = 2)
rownames(expression_scaled) = cell_ids
colnames(expression_scaled) = genes
ligand_activities = predict_single_cell_ligand_activities(cell_ids = cell_ids, expression_scaled = expression_scaled, ligand_target_matrix = ligand_target_matrix, potential_ligands = potential_ligands)
normalized_ligand_activities = normalize_single_cell_ligand_activities(ligand_activities)
## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.