Last data update: 2014.03.03
R: Exploratory visualization of information spread of biological...
plot.abstract.nodes R Documentation
Exploratory visualization of information spread of biological networks
Description
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.
Usage
## 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", ... )
Arguments
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.
Author(s)
Shailesh Tripathi, Frank Emmert-Streib
References
http://bio-complexity.com/
Examples
require(igraph)
data("PPI_Athalina")
data("modules_PPI_Athalina")
plot.abstract.nodes(g1, mod.list = lm,
edge.colors = c("red","green","blue","orange"))
Results
R version 3.3.1 (2016-06-21) -- "Bug in Your Hair"
Copyright (C) 2016 The R Foundation for Statistical Computing
Platform: x86_64-pc-linux-gnu (64-bit)
R is free software and comes with ABSOLUTELY NO WARRANTY.
You are welcome to redistribute it under certain conditions.
Type 'license()' or 'licence()' for distribution details.
R is a collaborative project with many contributors.
Type 'contributors()' for more information and
'citation()' on how to cite R or R packages in publications.
Type 'demo()' for some demos, 'help()' for on-line help, or
'help.start()' for an HTML browser interface to help.
Type 'q()' to quit R.
> library(netbiov)
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
> png(filename="/home/ddbj/snapshot/RGM3/R_BC/result/netbiov/plot.abstract.nodes.Rd_%03d_medium.png", width=480, height=480)
> ### Name: plot.abstract.nodes
> ### Title: Exploratory visualization of information spread of biological
> ### networks
> ### Aliases: plot.abstract.nodes
>
> ### ** Examples
>
> require(igraph)
> data("PPI_Athalina")
> data("modules_PPI_Athalina")
> plot.abstract.nodes(g1, mod.list = lm,
+ edge.colors = c("red","green","blue","orange"))
$g
IGRAPH UNW- 24 41 --
+ attr: name (v/c), label (v/c), weight (e/n)
+ edges (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 -9.922799 -7.101355
GO:0009639 5.257291 30.410693
GO:0009736 35.983771 -10.218641
GO:0006352 10.959543 -41.311221
GO:0045036 -35.417103 33.035643
GO:0031123 -48.941435 -8.152928
GO:0009738 43.128044 37.748850
GO:0009742 -17.591155 -63.267412
GO:0051726 71.000824 5.580208
GO:0008380 51.686475 -50.060960
GO:0006355 -58.922101 -43.324444
GO:0006810 -30.988881 73.053596
GO:0031667 30.386976 76.775930
GO:0007389 -81.085898 26.760723
GO:0030968 24.581713 -93.937711
GO:0007243 -1.886630 100.000000
GO:0010374 -100.000000 -12.034310
GO:0006913 -75.311003 69.927969
GO:0009626 100.000000 -25.165001
GO:0010087 -30.819373 -100.000000
GO:0015979 99.106623 35.051830
GO:0051252 73.932334 77.315089
GO:0044257 -81.329380 -73.858667
GO:0071472 79.091715 -77.189747
$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"
>
>
>
>
>
> dev.off()
null device
1
>
providing 
.