plot_targets_and_regulators: Updated plot of top regulators given targets in dynamic...

In pcahan1/epoch: Dynamic GRN reconstruction from single cell RNA-Seq data

Description

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.

Usage

plot_targets_and_regulators(
  grn,
  targets,
  epochs = NULL,
  weight_column = "zscore",
  gene_ranks = NULL,
  numTopRegulators = 5,
  order = NULL,
  fixed_layout = TRUE,
  declutter = TRUE,
  show_expression = TRUE,
  node_size = 5,
  label_size = 2,
  title_size = 10,
  legend_size = 8
)

Arguments

grn	the result of running epochGRN
targets	targets
epochs	result of running assign_epochs
weight_column	column name containing reconstruction weights to use
numTopRegulators	number of top regulators to plot
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.

pcahan1/epoch documentation built on Feb. 14, 2022, 1:57 a.m.