build_rl_network: Identifies all R / L interactions

In kgellatl/SignallingSingleCell: Network Analysis for single cell RNA sequencing Data (sc-RNASeq)

Description

This function will map all RL interactions

Usage

build_rl_network(
  input,
  value = "log10_Connection_product",
  group_by = FALSE,
  merge_all = F,
  comparitive = FALSE,
  from = FALSE,
  to = FALSE,
  input_full = NA,
  write_interactive = TRUE,
  interactive_groups = "nodes",
  nodesize = 3,
  size_by_connections = TRUE,
  textsize = 0.5,
  h = 8,
  w = 8,
  prefix = ""
)

Arguments

input	the input networked (usually filtered)
value	the column of the full network to calculate foldChange on
group_by	the pData columns calc_rl_network was calculated on to split the networks
comparitive	If true will look at connections across group_by and color edges by their change
from	the comparitive reference
to	the condition to compare to reference
input_full	the input full network
write_interactive	whether or not to write an interactive visNetwork html object
interactive_groups	the dropdown menu for selection nodes, either "nodes", "group_by", or "cluster"
nodesize	The size of nodes
size_by_connections	if true will override node size and size by the degree of the node
textsize	The size of text
h	pdf height
w	pdf width
prefix	a character to be appeneded to the start of file names into independent networks

Details

This will use the calc_agg_bulk results to ID networks

Examples

ex_sc_example <- id_rl(input = ex_sc_example)

kgellatl/SignallingSingleCell documentation built on Dec. 29, 2021, 4:12 p.m.