evolution,network-method {Cascade}

R Documentation

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 signature '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
)

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

Value

A HTML page with the evolution of the network.

Author(s)

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

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

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