plotweb {bipartite}R Documentation

Visualize a bipartite interaction matrix (e.g. a foodweb)

Description

A two dimensional matrix is plotted as a bipartite graph.

Usage

plotweb(web, method = "cca", empty = TRUE, labsize = 1, ybig = 1,
    y_width = 0.1, spacing = 0.05, arrow="no", col.interaction="grey80",
    col.pred = "grey10", col.prey="grey10", lab.space=1,
    bor.col.interaction ="black", bor.col.pred="black", bor.col.prey="black",
    lablength = NULL, sequence=NULL, low.abun=NULL, low.abun.col="green",
    bor.low.abun.col ="black", 
    high.abun=NULL, high.abun.col="red", bor.high.abun.col="black",
    text.rot=0, text.high.col="black", text.low.col="black")

Arguments

web Web is a matrix representing the interactions observed between higher trophic level species (columns) and lower trophic level species (rows). Usually this will be number of pollinators on each species of plants or number of parasitoids on each species of prey.
method Default method is cca, which leads to as few crossings of interactions as possible. The other option is normal, which leaves order as given by the matrix.
empty logical; should empty columns or empty rows be omitted from plotting; defaults to true
labsize factor for size of labels, default is 1
ybig vertical distance between upper and lower boxes, default is 1
y_width width of upper and lower boxes, default is 0.1
spacing horizonatal distance between upper and lower boxes, default is 0.05
arrow display type of connection between upper and lower boxes, options are up, down, both, up.center, down.center, both.center and no, default is no, which is a polygonal connection between boxes.
col.interaction color of interaction, default is grey80.
col.pred color of upper boxes, default is grey10.
col.prey color of lower boxes, default is grey10.
lab.space sometimes it is neccessary to add additional space for labels below und above of the boxes, so all labes are shown, default is 1.
bor.col.interaction border color of interaction, default is black
bor.col.pred border color of upper boxes, default is black
bor.col.prey border color of lower boxes, default is black
lablength number of characters of labels that should be plotted. If zero no labels are shown, default is NULL which plots the complete labels.
sequence list of two with two names vectors: seq.pred and seq.prey, which specify the order in which species are plotted. Cannot be set for method="cca". Defaults to NULL, where the sequence remains as given or is determined by the CCA internally.
low.abun Vector with independent abundance estimates for the lower trophic level, NULL if none exists.
low.abun.col Colour for depicting the abundance estimates for the lower trophic level; defaults to green.
bor.low.abun.col border color for depicting the abundance estimates for the lower trophic level, default is black
high.abun Vector with independent abundance estimates for the higher trophic level, NULL if none exists.
high.abun.col Colour for depicting the abundance estimates for the lower trophic level; defaults to red.
bor.high.abun.col border color for depicting the abundance estimates for the higher trophic level, default is black
text.rot orientation of labels in the plot (to avoid overlapping of horizontal labels if dimension of the webs are high), default is 0 for horizontal labels, use text.rot=90 for vertical labels.
text.high.col Colour for text labels of higher trophic level, a vector of colours can be given
text.low.col Colour for text labels of lower trophic level. A vector of colours can be given

Value

Returns a window with a bipartite graph of a foodweb. For all colours vectors can be used (which are recycled if length differs.

Author(s)

Bernd Gruber bernd.gruber@ufz.de

References

Tylianakis, J. M., Tscharntke, T. and Lewis, O. T. (2007) Habitat modification alters the structure of tropical host-parasitoid food webs. Nature 445, 202–205

See Also

For a different plot of foodwebs see visweb

Examples

data(Safariland)
plotweb(Safariland)

# shorter labels
plotweb(Safariland, lablength=3, arrow="down")

# centered triangles for displaying interacions
plotweb(Safariland, text.rot=90, arrow="down.center", col.interaction="wheat2")

#orginal sequence, up arrows and different box width
plotweb(Safariland, method="normal", arrow="up", y_width=0.3, lablength=4)
# interactions as lines
plotweb(Safariland, arrow="both", y_width=0.05, text.rot=90, col.pred="blue", col.prey="green")

# add an abundance vector for lower trophic species 
low.abun = round(runif(dim(Safariland)[1],1,40)) #create
names(low.abun) <- rownames(Safariland)
plotweb(Safariland, text.rot=90, low.abun=low.abun, col.interaction="purple", y_width=0.05)

plotweb(Safariland, text.rot=90, low.abun=low.abun, col.interaction ="red", bor.col.interaction="red", arrow="down")

# now vectors for all colours can be given, to mark certain species or interactions. Colour vectors are recycled if not of appropriate length
plotweb(Safariland,col.pred=c("orange","green"))
plotweb(Safariland,col.pred=c("orange","green"),col.prey=c("white","grey","purple"),text.high.col=c("blue","red"), col.interaction=c("red",rep("green",26),rep("brown",242)), bor.col.interaction=c(rep("green",26),rep("brown",242)),method="normal", text.rot=90, lablength=10)



[Package bipartite version 0.90 Index]