plot.abstract.nodes {netbiov} | R Documentation |
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 |
|
mod.list |
|
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. |
... |
|
Shailesh Tripathi, Frank Emmert-Streib
require(igraph) data("PPI_Athalina") data("modules_PPI_Athalina") plot.abstract.nodes(g1, mod.list = lm, edge.colors = c("red","green","blue","orange"))