Export an interactive HTML browser of individual TF regulons

Usage

report_top_tf_targets(
  module2,
  output_dir,
  tfs,
  top_n = 100L,
  default_top_n = NULL,
  verbose = TRUE,
  multiomic_data = NULL,
  conditions = NULL,
  combine_tfs = FALSE,
  default_condition = NULL,
  max_linked_tfs = 50L,
  max_linked_tfs_per_target = 2L,
  supporting_module2 = NULL,
  default_fp_r_cutoff = 0.5,
  expression_pseudocount = 1,
  target_genes = NULL
)

Arguments

module2: Module 2 result list, loaded output list, or output directory.
output_dir: Output directory.
tfs: TFs to report.
top_n: Number of top targets per TF.
default_top_n: Initial number of targets displayed in the browser. The default displays the complete embedded target set.
verbose: Emit concise progress messages.
multiomic_data: Optional CraftGRN multiomic object used to precompute condition activity and expression for the browser.
conditions: Optional conditions to include. The default includes all conditions available in `multiomic_data`.
combine_tfs: Combine all requested TFs into one global target-union browser. The default writes one browser per TF.
default_condition: Initial condition shown by the browser.
max_linked_tfs: Maximum number of non-seed supporting TFs.
max_linked_tfs_per_target: Maximum supporting TFs retained per target.
supporting_module2: Optional full Module 2 result or output directory used only to add non-seed TFs regulating the selected seed-TF targets.
default_fp_r_cutoff: Initial strict FP R cutoff shown by the browser.
expression_pseudocount: Pseudocount for differential node log2 fold changes.
target_genes: Optional target-gene subset embedded in each TF browser. The default ranks all predicted targets before applying `top_n`. Use `top_n = Inf` to retain the complete predicted or supplied target set.

Value

A tibble report manifest.