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". This method thus does not to calculate node similarity based on inward/outward link similarity.

Usage

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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 <haydi@126.com>

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

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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)

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