plot.abstract.nodes: Exploratory visualization of information spread of biological...
In netbiov: A package for visualizing complex biological network

Description Usage Arguments Author(s) References Examples

Modular layout style:

Visualization of modules in an abstract way. In the function plot.abstract.nodes, nodes in a module are replaced by a single node and the relative size of a node is proportional to the total number of nodes in a module. In the functions plot.abstract.module, plot.abstract.nodes, edges between two modules are replaced by a single edge and the total number of edges between two modules are reflected by the relative edge-width.

## S3 method for class 'abstract.nodes'
plot(x, mod.list=NULL,  rest.module=TRUE, 
color.random=FALSE, nodes.color = NULL, edge.colors=NULL,
layout.function=NULL,tkplot=FALSE,v.sf = 0, e.sf = 0,lab.color=NULL,
lab.cex=NULL, lab.dist=NULL, bg="black", ... )

`x`	`x` is a graph object created from an adjacency matrix or from a tabular data of two columns using `graph()` function available in `igraph`
`mod.list`	`mod.list` is a list object each components of mod.list consists a vector of module to be plotted.
`random`	is a logical value, if modules information is not provided then random nodes for the modules are selected.
`rest.module`	is a logical value, rest of the nodes to be plotted as a one module (if TRUE) or independently (if FALSE)
`color.random`	is a logical value, if this option is TRUE it will assign random color to each module or nodes.
`nodes.color`	assigns colors to nodes of recreated graph
`edge.colors`	is a vector of colors, assigned to color edges depending on their width from small to large width.
`layout.function`	is a function class, this corrosponds to a layout function given as an input to plot a graph. Input function should return a two column matrix which has same no of rows as the modules in the graph
`tkplot`	is a boolean variable, if it is true function will use this option to plot a graph, if it is false function will use plot function with a black background.
`v.sf`	is a numeric value, this option to increase or decrease the size of nodes
`e.sf`	is a numeric value, this option to increase or decrease width of edges
`lab.color`	colors the vertices and edge labels
`lab.cex`	is anumeric value, increase or decrease the font size of labels
`lab.dist`	is a numeric value, adjust vertex labels
`bg`	is a color value to adjust background color of the plot.
`...`	`...` parameter for other inputs.

Shailesh Tripathi, Frank Emmert-Streib

http://bio-complexity.com/

  require(igraph)
  data("PPI_Athalina")
  data("modules_PPI_Athalina")
  plot.abstract.nodes(g1, mod.list = lm, 
edge.colors = c("red","green","blue","orange"))

Loading required package: igraph

Attaching package: 'igraph'

The following objects are masked from 'package:stats':

    decompose, spectrum

The following object is masked from 'package:base':

    union

$g
IGRAPH c813c0c UNW- 24 41 -- 
+ attr: name (v/c), label (v/c), weight (e/n)
+ edges from c813c0c (vertex names):
 [1] GO:0007126--GO:0009736 GO:0007126--GO:0009742 GO:0007126--GO:0007389
 [4] GO:0007126--GO:0009626 GO:0009639--GO:0009736 GO:0009639--GO:0045036
 [7] GO:0009639--GO:0031123 GO:0009639--GO:0009742 GO:0009639--GO:0051726
[10] GO:0009639--GO:0008380 GO:0009639--GO:0006355 GO:0009639--GO:0031667
[13] GO:0009639--GO:0030968 GO:0009639--GO:0007243 GO:0009639--GO:0009626
[16] GO:0009639--GO:0051252 GO:0009639--GO:0044257 GO:0009639--GO:0071472
[19] GO:0009736--GO:0009738 GO:0009736--GO:0010374 GO:0009736--GO:0006913
[22] GO:0009736--GO:0010087 GO:0006352--GO:0051726 GO:0006352--GO:0007243
+ ... omitted several edges

$layout
                  [,1]        [,2]
GO:0007126  -14.274637    8.575594
GO:0009639   11.736230  -18.130384
GO:0009736   29.509742   24.785702
GO:0006352  -14.613330  -47.376291
GO:0045036  -20.770866   46.709279
GO:0031123  -51.220338   -8.646884
GO:0009738   53.904631   -8.132650
GO:0009742   36.757380  -49.972797
GO:0051726   21.549732   61.469856
GO:0008380  -60.914829   32.820883
GO:0006355  -52.841479  -49.613491
GO:0006810   79.814859   30.575833
GO:0031667    9.021084  -85.756097
GO:0007389  -34.780052   86.976586
GO:0030968   81.694840  -51.880277
GO:0007243   67.048703   71.408066
GO:0010374  100.000000   -9.215476
GO:0006913   12.118861  100.000000
GO:0009626 -100.000000   13.286361
GO:0010087  -96.445091  -31.197401
GO:0015979  -29.433565 -100.000000
GO:0051252  -81.557466   68.924127
GO:0044257   52.149153  -93.421745
GO:0071472  -77.585108  -81.264057

$vertex.color
 GO:0007126  GO:0009639  GO:0009736  GO:0006352  GO:0045036  GO:0031123 
"#FFFF56BF" "#FF0200BF" "#FFF300BF" "#FFFF56BF" "#FFFF02BF" "#FFFFC0BF" 
 GO:0009738  GO:0009742  GO:0051726  GO:0008380  GO:0006355  GO:0006810 
"#FFEE00BF" "#FFFF0CBF" "#FFBB00BF" "#FFFD00BF" "#FFDB00BF" "#FFFF7BBF" 
 GO:0031667  GO:0007389  GO:0030968  GO:0007243  GO:0010374  GO:0006913 
"#FFFFD3BF" "#FFFF84BF" "#FFFFE6BF" "#FFFFDCBF" "#FFFFA9BF" "#FFFF92BF" 
 GO:0009626  GO:0010087  GO:0015979  GO:0051252  GO:0044257  GO:0071472 
"#FFFFA9BF" "#FFFF51BF" "#FFFF76BF" "#FFFFC0BF" "#FFFFE1BF" "#FFFFA0BF" 

$edge.color
 [1] "orange" "red"    "red"    "red"    "orange" "blue"   "blue"   "blue"  
 [9] "blue"   "red"    "red"    "orange" "blue"   "blue"   "blue"   "blue"  
[17] "blue"   "orange" "red"    "orange" "red"    "orange" "red"    "red"   
[25] "red"    "orange" "red"    "red"    "blue"   "red"    "red"    "red"   
[33] "red"    "red"    "red"    "red"    "red"    "red"    "red"    "red"   
[41] "red"   

$vertex.size
GO:0007126 GO:0009639 GO:0009736 GO:0006352 GO:0045036 GO:0031123 GO:0009738 
  18.86842   59.00000   24.78947   18.86842   22.81579   13.82456   25.44737 
GO:0009742 GO:0051726 GO:0008380 GO:0006355 GO:0006810 GO:0031667 GO:0007389 
  22.37719   32.68421   23.25439   28.07895   17.11404   11.85088   16.67544 
GO:0030968 GO:0007243 GO:0010374 GO:0006913 GO:0009626 GO:0010087 GO:0015979 
  10.97368   12.50877   14.92105   16.01754   14.92105   19.08772   17.33333 
GO:0051252 GO:0044257 GO:0071472 
  13.82456   11.19298   15.35965 

$edge.arrow.size
[1] 0.3

$vertex.label.cex
[1] 1

$vertex.label
 [1] "GO:0007126 \ntotal nodes: 45"  "GO:0009639 \ntotal nodes: 228"
 [3] "GO:0009736 \ntotal nodes: 72"  "GO:0006352 \ntotal nodes: 45" 
 [5] "GO:0045036 \ntotal nodes: 63"  "GO:0031123 \ntotal nodes: 22" 
 [7] "GO:0009738 \ntotal nodes: 75"  "GO:0009742 \ntotal nodes: 61" 
 [9] "GO:0051726 \ntotal nodes: 108" "GO:0008380 \ntotal nodes: 65" 
[11] "GO:0006355 \ntotal nodes: 87"  "GO:0006810 \ntotal nodes: 37" 
[13] "GO:0031667 \ntotal nodes: 13"  "GO:0007389 \ntotal nodes: 35" 
[15] "GO:0030968 \ntotal nodes: 9"   "GO:0007243 \ntotal nodes: 16" 
[17] "GO:0010374 \ntotal nodes: 27"  "GO:0006913 \ntotal nodes: 32" 
[19] "GO:0009626 \ntotal nodes: 27"  "GO:0010087 \ntotal nodes: 46" 
[21] "GO:0015979 \ntotal nodes: 38"  "GO:0051252 \ntotal nodes: 22" 
[23] "GO:0044257 \ntotal nodes: 10"  "GO:0071472 \ntotal nodes: 29" 

$lab.color
[1] "blue"

$lab.dist
[1] 0.2

$vertex.frame.color
 GO:0007126  GO:0009639  GO:0009736  GO:0006352  GO:0045036  GO:0031123 
"#FFFF56BF" "#FF0200BF" "#FFF300BF" "#FFFF56BF" "#FFFF02BF" "#FFFFC0BF" 
 GO:0009738  GO:0009742  GO:0051726  GO:0008380  GO:0006355  GO:0006810 
"#FFEE00BF" "#FFFF0CBF" "#FFBB00BF" "#FFFD00BF" "#FFDB00BF" "#FFFF7BBF" 
 GO:0031667  GO:0007389  GO:0030968  GO:0007243  GO:0010374  GO:0006913 
"#FFFFD3BF" "#FFFF84BF" "#FFFFE6BF" "#FFFFDCBF" "#FFFFA9BF" "#FFFF92BF" 
 GO:0009626  GO:0010087  GO:0015979  GO:0051252  GO:0044257  GO:0071472 
"#FFFFA9BF" "#FFFF51BF" "#FFFF76BF" "#FFFFC0BF" "#FFFFE1BF" "#FFFFA0BF" 

$edge.width
 [1]  5.000000  1.666667  1.666667  1.666667  5.000000  3.333333  3.333333
 [8]  3.333333  3.333333  1.666667  1.666667 10.000000  3.333333  3.333333
[15]  3.333333  3.333333  3.333333  8.333333  1.666667  5.000000  1.666667
[22]  5.000000  1.666667  1.666667  1.666667  5.000000  1.666667  1.666667
[29]  3.333333  1.666667  1.666667  1.666667  1.666667  1.666667  1.666667
[36]  1.666667  1.666667  1.666667  1.666667  1.666667  1.666667

$bg
[1] "black"

$vertex.label.family
[1] "serif"

$edge.label.color
[1] "blue"

$edge.label.cex
[1] 1

$edge.curved
[1] FALSE

attr(,"class")
[1] "netbiov"