groupplot: A group 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

This function is for plotting different graphs into a same map with different colors, line styles and so on. 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

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

Arguments

gemat	standard graph square matrix
groups	must be a list, each list element has the species that belong to a same group.
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.
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,

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)
glist<-list(c1=c(1:5),c2=c(1,3),c3=c(3,4,5))
pch=c(21,21,21) #length of the parameter vector should be identical to the number of species groups
bg=c(1,2,3)
lcol=c(8,2,4)
groupplot(gemat=mat,groups=glist,pch=pch,lcol=lcol,bg=bg) #other parameters are set in default

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