See the evolution of the network with change of cutoff — evolution,network-method • Cascade

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.

# 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
)

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.

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.

Author

Nicolas Jung, Frédéric Bertrand , Myriam Maumy-Bertrand.

Examples


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