fplot: Another way to plot network structure based on similar vertex...

In loop: loop decomposition of weighted directed graphs for life cycle analysis, providing flexbile network plotting methods, and analyzing food chain properties in ecology

Description

The method for seperating the nodes in the two-dimensional spaces is the non-dimensional scaling technique, which can take the similarity matrices of the nodes as the input and generate the positions of the nodes in the space.

Usage

fplot(gemat,type="both",metric="jaccard",addlabels=FALSE,scaled=TRUE,weighted=TRUE,pch=20,bg=1,pcex=3,pcol=4,lty=1,lcol=8,tfont=12,tcol=1)

Arguments

gemat	standard graph square matrix
type	if type="both", the node similarity is calculated based on the the vertex similarity from the inward/outward links for each pair of nodes. if type="in", the node similarity is calculated based on the the vertex similarity from the inward links for each pair of nodes. if type="out", the node similarity is calculated based on the the vertex similarity from the outward links for each pair of nodes.
metric	node similarity methods, currently supporting two basic similarity indices: "jaccard" and "sorensen".
addlabels	if you want to label each node/vertex, set it's status as TRUE; default is FALSE
scaled	if you want to the links showing relative weights, set it's status as TRUE; default is FALSE links with larger weights will have thicker line width, vice versa.
weighted	if TRUE, the links/edges will be weighted based on the cell value present in the matrix of gemat, different edges then will have different line widths for representing them. Otherwise, all edges have the same line width. Default is TRUE
pch	this pch is for nodes/vertex
bg	bg is for nodes/vertex filled background colors, will function when pch=21:25.
pcex	pcex is for nodes/vertex size
pcol	pcol is for nodes/vertex color
lty	lty is the line style for the links
lcol	lcol is the line color for the links
tfont	tfont is the font size for the labels of the nodes
tcol	tcol is the color for the labels of the nodes

Author(s)

Youhua Chen <[e-mail]>

References

Chen Y (2012) loop: an R package for performing decomposition of weighted directed graphs, food web analysis and flexible network plotting. Submitted.

See Also

fplot.foodweb, groupplot.foodweb, gplot, gplot1, groupplot

Examples

mat=matrix(c(0,5,3,7,0,5,0,8,0,4,3,8,0,1,6,7,0,1,0,2,0,4,6,2,0),5,5)
fplot(gemat=mat) #other parameters are set in default

Example output

Loading required package: grid
Loading required package: MASS
initial  value 0.000000 
final  value 0.000000 
converged

loop documentation built on May 2, 2019, 9:07 a.m.