plot_tf_network: Function to visualize transcription factors regulatory...

In jiang-junyao/IReNA: IReNA

Function to visualize transcription factors regulatory network

Description

This function integrate R package igraph to visualize consequence of regulatory network analysis

Usage

plot_tf_network(
  TFs_list,
  layout = "grid",
  group.cols = NULL,
  title.name = NULL,
  vertex.size = 13,
  vertex.size.add = 3,
  vertex.label.color = "black",
  edge.label.color = "black",
  legend = TRUE,
  vertex.label.cex = 0.8,
  vertex.label.family = "ArialMT",
  frame.color = "white",
  arrow.size = 0.2,
  arrow.width = 0.5,
  edge.width = 1.8,
  edge.curved = 0,
  edge.color = c("#FDD1B0", "#B3B3B3")
)

Arguments

TFs_list	TFs_list generated by network_analysis
layout	the layout to display the network, options: 'grid','sphere', 'circle','random'
group.cols	colors for group in network
title.name	the name of the title
vertex.size	size of vertex whose edge numbers are last 25%
vertex.size.add	expansion size of vertex whose edge numbers are last 25%-75% and top25%
vertex.label.color	ertex label color
edge.label.color	edge label color
legend	logic, indicating whether to show the legend
vertex.label.cex	The label size of vertex
vertex.label.family	vertex label family
frame.color	frame.color
arrow.size	arrow size
arrow.width	arrow width
edge.width	edge width
edge.curved	edge curvature
edge.color	edge color. You need to input two colors, first one indicate 'Positive' regulation, second one indicate 'Negative' regulation.

Value

figure

Examples

#'
load(system.file("extdata", "test_clustering.rda", package = "IReNA"))
Kmeans_clustering <- add_ENSID(test_clustering, Spec1 = "Hs")
cor0.6 <- get_cor(Kmeans_clustering, Tranfac201803_Hs_MotifTFsF, 0.7, start_column=3)
TFs_list <- network_analysis(cor0.6,Kmeans_clustering)
plot_tf_network(TFs_list)

jiang-junyao/IReNA documentation built on Nov. 4, 2024, 8:29 p.m.