Plot — plot-methods • Cascade

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

# S4 method for micro_array,ANY
plot(x, y, ...)

# S4 method for network,ANY
plot(
  x,
  y,
  choice = "network",
  nv = 0,
  gr = NULL,
  ini = NULL,
  color.vertex = NULL,
  video = TRUE,
  weight.node = NULL,
  ani = FALSE,
  taille = c(2000, 1000),
  label_v = 1:dim(x@network)[1],
  horiz = TRUE,
  legend.position = "topleft",
  frame.color = "black",
  label.hub = FALSE,
  ...
)

# S4 method for micropredict,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 micro_array object, a network object or a micropredict 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.
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?
taille: 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.
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 = \"micro_array\", y = \"ANY\",...)")

x: a micro_array object
list_nv: a vector of cutoff at which the network should be shown

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

x

a 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: animated plot?
size: vector giving the size of the plot. Default to c(2000,1000)
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 = \"micropredict\", y = \"ANY\",...)")

x: a micropredict object
list(): Optionnal arguments: see plot for network

Examples


data(Net)
plot(Net)
#> Loading required package: igraph
#> 
#> Attaching package: ‘igraph’
#> The following object is masked from ‘package:Cascade’:
#> 
#>     compare
#> The following objects are masked from ‘package:stats’:
#> 
#>     decompose, spectrum
#> The following object is masked from ‘package:base’:
#> 
#>     union


data(M)
plot(M)








data(Selection)
data(network)
nv<-0.11
plot(network,choice="network",gr=Selection@group,nv=nv,label_v=Selection@name,
edge.arrow.size=0.9,edge.thickness=1.5)