Cascade (version 2.1)

evolution,network-method: See the evolution of the network with change of cutoff

Description

See the evolution of the network with change of cutoff. This function may be usefull to see if the global topology is changed while increasing the cutoff.

Usage

# S4 method for network
evolution(
  net,
  list_nv,
  gr = NULL,
  color.vertex = NULL,
  fix = TRUE,
  gif = TRUE,
  taille = c(2000, 1000),
  label_v = 1:dim(net@network)[1],
  legend.position = "topleft",
  frame.color = "black",
  label.hub = FALSE
)

Value

A HTML page with the evolution of the network.

Arguments

net

a network object

list_nv

a vector of cutoff at which the network should be shown

gr

a vector giving the group of each gene

color.vertex

a vector giving the color of each node

fix

logical, should the position of the node in the network be calculated once at the beginning ? Defaults to TRUE.

gif

logical, TRUE

taille

vector giving the size of the plot. Default to c(2000,1000)

label_v

(optional) the name of the genes

legend.position

(optional) the position of the legend, defaults to "topleft"

frame.color

(optional) the color of the frame, defaults to "black"

label.hub

(optional) boolean, defaults to FALSE

Author

Nicolas Jung, Frédéric Bertrand , Myriam Maumy-Bertrand.

References

Jung, N., Bertrand, F., Bahram, S., Vallat, L., and Maumy-Bertrand, M. (2014). Cascade: a R-package to study, predict and simulate the diffusion of a signal through a temporal gene network. Bioinformatics, btt705.

Vallat, L., Kemper, C. A., Jung, N., Maumy-Bertrand, M., Bertrand, F., Meyer, N., ... & Bahram, S. (2013). Reverse-engineering the genetic circuitry of a cancer cell with predicted intervention in chronic lymphocytic leukemia. Proceedings of the National Academy of Sciences, 110(2), 459-464.

Examples

# \donttest{
	data(network)
	sequence<-seq(0,0.2,length.out=20)
	#setwd("inst/animation")
	#evolution(network,sequence)
# }