groupplot.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". "groups" are a list for each list element showing a group of species. They should be defined based on the user's choices. This method thus does not to calculate node similarity based on inward/outward link similarity.

Usage

groupplot.foodweb(gemat, ranks, groups, addlabels = FALSE, scaled = TRUE, pch = 20, bg = 1, pcex = 3, pcol = 4, lty = 1, lcol = 8, tfont = 12, tcol = 1)

Arguments

gemat	standard square graph matrix
ranks	a list for each list memember showing the species in that rank (list number). for example list[[1]] means all the species in food web hierarchy rank 1, and so on...
groups	a list of species groups. Can be overlapped among the list elements. But should be defined by the users.
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, gplot, gplot1, 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)
glist<-list(c1=c(1:5),c2=c(1,2,3),c3=c(2,4,5))
groupplot.foodweb(gemat=mat,ranks=rlist,groups=glist) #other parameters are set in default
#when not setting other parameters, the groupplot result is identical to fplot
#because the function found that the parameters (especially the colors) are not set
#another example that can separate the groups
rlist<-list(c1=c(1,2),c2=c(3,4),c3=5)
glist<-list(c1=c(1:5),c2=c(1,3),c3=c(3,4,5))
pch=c(20,22,24) #length of the parameter vector should be identical to the number of species groups
lcol=c(8,2,4)
groupplot.foodweb(gemat=mat,ranks=rlist,groups=glist,pch=pch,lcol=lcol) #other parameters are set in default

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