This function calculates a signaling network. It requires a domino object preprocessed from create_domino and returns a domino object prepared for plotting with the various plotting functions in this package.
Usage
build_domino(
dom,
max_tf_per_clust = 5,
min_tf_pval = 0.01,
max_rec_per_tf = 5,
rec_tf_cor_threshold = 0.15,
min_rec_percentage = 0.1
)Arguments
- dom
Domino object from
create_domino().- max_tf_per_clust
Maximum number of transcription factors called active in a cluster.
- min_tf_pval
Minimum p-value from differential feature score test to call a transcription factor active in a cluster.
- max_rec_per_tf
Maximum number of receptors to link to each transcription factor.
- rec_tf_cor_threshold
Minimum Spearman correlation used to consider a receptor linked with a transcription factor. Increasing this will decrease the number of receptors linked to each transcription factor.
- min_rec_percentage
Minimum percentage of cells in cluster expressing a receptor for the receptor to be linked to trancription factors in that cluster.
Examples
example(create_domino, echo = FALSE)
#a relaxed example
pbmc_dom_built_tiny <- build_domino(
dom = pbmc_dom_tiny, min_tf_pval = .05, max_tf_per_clust = Inf,
max_rec_per_tf = Inf, rec_tf_cor_threshold = .1, min_rec_percentage = 0.01
)