plot-methods {Patterns}

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)
}