Cascade: evolution-network-method – R documentation

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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 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`	(optionnal) the name of the genes
`legend.position`	(optionnal) the position of the legend, defaults to "topleft"
`frame.color`	(optionnal) the color of the frame, defaults to "black"
`label.hub`	(optionnal) 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)

Cascade

Selection, Reverse-Engineering and Prediction in Cascade Networks

v2.0

GPL (>= 2)

Authors

Frederic Bertrand [cre, aut] (<https://orcid.org/0000-0002-0837-8281>), Myriam Maumy-Bertrand [aut] (<https://orcid.org/0000-0002-4615-1512>), Laurent Vallat [ctb], Nicolas Jung [ctb]

Initial release

2021-03-18