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loop (version 1.1)

fplot.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". 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

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

Run this code
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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