fplot.foodweb: a special group graph plot function for food web-style...

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

vertex/nodes/species are arranged in a form of vertical hierarchy, given the species' food rank positions listed in the parameter "ranks". This method thus does not to calculate node similarity based on inward/outward link similarity.

Usage

fplot.foodweb(gemat,ranks,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 square graph matrix
ranks	must be a list, each list element represented the species in that given rank (list number order), for example list[[1]] means all the species in food web hierarchy rank 1, and so on...
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, groupplot.foodweb, fplot, 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)
rlist<-list(c1=c(1,2),c2=c(3,4),c3=5)
#other parameters are set in default
fplot.foodweb(gemat=mat,ranks=rlist)
#change some parameters
fplot.foodweb(gemat=mat,ranks=rlist,lcol=3,pch=21,
bg="white",addlabels=TRUE,tfont=5)

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