Updated plot of top regulators given targets in dynamic networks based on a weight column. Top regulators computed for each epoch, but maintained in plot across epochs if present in epoch subnetwork.

plot_targets_and_regulators(
  network,
  targets,
  epochs = NULL,
  weight_column = "weight",
  gene_ranks = NULL,
  regulators_num = 5,
  network_order = NULL,
  fixed_layout = TRUE,
  declutter = TRUE,
  show_expression = TRUE,
  node_size = 5,
  label_size = 2,
  title_size = 10,
  legend_size = 8
)

Arguments

network: the result of running epochGRN
targets: targets
epochs: result of running assign_epochs
weight_column: column name containing reconstruction weights to use
gene_ranks: gene_ranks
regulators_num: number of top regulators to plot
network_order: which epochs or transitions to plot
fixed_layout: whether or not to fix node positions across epoch networks
declutter: if TRUE, will only label nodes with active interactions in given network
show_expression: if TRUE, size and shade of node indicates mean expression in a given epoch.
node_size: node_size
label_size: label_size
title_size: title_size
legend_size: legend_size

Value

plot