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

In Patterns: Deciphering Biological Networks with Patterned Heterogeneous Measurements

See the evolution of the network with change of cutoff

Description

See the evolution of the network with change of cutoff

Usage

## S4 method for signature '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"

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

Value

A HTML page with the evolution of the network.

Author(s)

Bertrand Frederic, Myriam Maumy-Bertrand.

Examples

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)


## Not run: 
#Example of use of the evolution method with an animated gif output.
evolution(network,sequence,type.ani = "gif", outdir=destdir)

## End(Not run)

Patterns documentation built on Dec. 1, 2022, 5:09 p.m.