bipartite (version 0.90)

plotweb: 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

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, defaul

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

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.

encoding

latin1

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)