loop (version 1.1)

groupplot.foodweb: a special group graph plot function for food web-style hierarchical structure

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

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