plot-methods: Plot

In fbertran/Patterns: Deciphering Biological Networks with Patterned Heterogeneous Measurements

Plot

Description

Considering the class of the argument which is passed to plot, the graphical output differs.

Usage

## S4 method for signature 'omics_array,ANY'
plot(x, y, ...)

## S4 method for signature 'omics_network,ANY'
plot(
  x,
  y,
  choice = "omics_network",
  nv = 0,
  gr = NULL,
  ini = NULL,
  color.vertex = NULL,
  color.edge = NULL,
  video = TRUE,
  weight.node = NULL,
  ani = FALSE,
  size = c(2000, 1000),
  label_v = 1:dim(x@omics_network)[1],
  horiz = TRUE,
  legend.position = "topleft",
  frame.color = "black",
  label.hub = FALSE,
  nround = 2,
  ani.img.name = "Rplot",
  ani.imgdir = "images",
  ani.htmlfile = "index.html",
  outdir,
  ani.group.legend = "Cluster",
  layout = ini,
  alpha = 1,
  pixmap.color = terrain.colors(20),
  ...
)

## S4 method for signature 'omics_predict,ANY'
plot(
  x,
  time = NULL,
  label_v = NULL,
  frame.color = "white",
  ini = NULL,
  label.hub = FALSE,
  edge.arrow.size = 0.7,
  edge.thickness = 1
)

Arguments

x	a omics_array object, a omics_network object or a omics_predict object
y	optional and not used if x is an appropriate structure
...	additional parameters
choice	what graphic should be plotted: either "F" (for a representation of the matrices F) or "network".
nv	the level of cutoff. Defaut to '0'.
gr	a vector giving the group of each gene
ini	using the “position” function, you can fix the position of the nodes.
color.vertex	a vector defining the color of the vertex.
color.edge	color of the edges
video	if ani is TRUE and video is TRUE, the result of the animation is saved as an animated GIF.
weight.node	nodes weighting. Defaults to 'NULL'.
ani	animated plot?
size	vector giving the size of the plot. Default to 'c(2000,1000)'.
label_v	vector defining the vertex labels.
horiz	landscape? Defaults to 'TRUE'.
legend.position	position of the legend.
frame.color	color of the frames.
label.hub	logical ; if TRUE only the hubs are labeled.
nround	number of digits to display
ani.img.name	name of image file for animations
ani.imgdir	name of the image directory for animations
ani.htmlfile	name of the html file for animations
outdir	name of the outdir for animations
ani.group.legend	legend for animations
layout	layout of the graphs
alpha	transparency of the graphs
pixmap.color	color for pixmap graphs
time	sets the time for plot of the prediction. Defaults to 'NULL'
edge.arrow.size	size of the arrows ; default to 0.7.
edge.thickness	edge thickness ; default to 1.

Methods

list("signature(x = \"omics_array\", y = \"ANY\",...)")

x

a omics_array object

list_nv

a vector of cutoff at which the network should be shown

list("signature(x = \"omics_network\", y = \"ANY\",...)")

x

a omics_network object

list()

Optionnal arguments:

gr

a vector giving the group of each gene

choice

what graphic should be plotted: either "F" (for a representation of the matrices F) or "network".

nv

the level of cutoff. Defaut to 0.

ini

using the “position” function, you can fix the position of the nodes

color.vertex

a vector defining the color of the vertex

ani

vector giving the size of the plot. Default to c(2000,1000). The animation can only be created in the working directory. See the help page of the animation method.

video

if ani is TRUE and video is TRUE, the animation result is a GIF video

label_v

vector defining the vertex labels

legend.position

position of the legend

frame.color

color of the frames

label.hub

logical ; if TRUE only the hubs are labeled

edge.arrow.size

size of the arrows ; default to 0.7

edge.thickness

edge thickness ; default to 1.

list("signature(x = \"omics_predict\", y = \"ANY\",...)")

x

a omics_predict object

list()

Optional arguments: see plot for omics_network

Author(s)

Bertrand Frederic, Myriam Maumy-Bertrand.

Examples

if(require(CascadeData)){
data(micro_US, package="CascadeData")
micro_US<-as.omics_array(micro_US[1:100,],time=c(60,90,210,390),subject=6)
plot(micro_US)
}

fbertran/Patterns documentation built on Dec. 8, 2022, 8:48 p.m.