See the evolution of the network with change of cutoff

# S4 method for omics_network
evolution(
  net,
  list_nv,
  gr = NULL,
  color.vertex = NULL,
  color.edge = NULL,
  fix = TRUE,
  size = c(2000, 1000),
  label_v = 1:dim(net@omics_network)[1],
  legend.position = "topleft",
  frame.color = "black",
  label.hub = FALSE,
  outdir,
  type.ani = "html"
)

Arguments

net: a omics_network object
list_nv: a vector of cutoff at which the network should be shown
gr: a vector giving the group of each genee. Defaults to NULL
color.vertex: a vector giving the color of each nodee. Defaults to NULL
color.edge: a vector giving the color of each edge. Defaults to NULL
fix: logical, should the position of the node in the network be calculated once at the beginning ? Defaults to TRUE.
size: vector giving the size of the plot. Defaults to c(2000,1000)
label_v: vector giving the labels of each vertex. Defaults to 1:dim(net@omics_network)[1]
legend.position: string giving the position of the legend. Defaults to "topleft"
frame.color: string giving the color of the frame of the plot. Defaults to "black"
label.hub: label hubs. Defaults to FALSE
outdir: Directory to save the animation. No default value since it must be specified by the user.
type.ani: Type of animation. Defaults to "html"
legend: string giving the position of the legend. Defaults to "topleft"

Value

A HTML page with the evolution of the network.

Details

Several types of outputs are available using the type.ani option.

html
latex (requires latex)
swf (requires swftools)
video (requires ffmpeg)
gif
manual_gif

Author

Bertrand Frederic, Myriam Maumy-Bertrand.

Examples


# \donttest{
data(network)
sequence<-seq(0,0.2,length.out=20)

#Change the destdir to have the animation created where you want. 
destdir = tempdir()

#Example of use of the evolution method with an html output.
evolution(network,sequence,type.ani = "html", outdir=destdir)
#> HTML file created at: index.html
# }

if (FALSE) {
#Example of use of the evolution method with an animated gif output.
evolution(network,sequence,type.ani = "gif", outdir=destdir)
}