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

In bipartite: Visualising Bipartite Networks and Calculating Some (Ecological) Indices

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.low = 0.1, 
    y.width.high = 0.1, low.spacing = NULL, high.spacing = NULL,
    arrow="no",  col.interaction="grey80", col.high = "grey10", 
    col.low="grey10",  bor.col.interaction ="black", bor.col.high="black", 
    bor.col.low="black", high.lablength = NULL, low.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", adj.high=NULL, adj.low=NULL, plot.axes = FALSE,
    low.y=0.5, high.y=1.5, add=FALSE, y.lim=NULL, x.lim=NULL, low.plot=TRUE, 
    high.plot=TRUE, high.xoff = 0, low.xoff = 0, high.lab.dis = NULL, 
    low.lab.dis = NULL, abuns.type="additional")

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.low	width of lower boxes, default is 0.1
y.width.high	width of upper boxes, default is 0.1
low.spacing	distance between lower boxes, default is NULL, so automatically spaced that length of upper and lower boxes is the same. Be aware if set to any value that x.lim may has to be adjusted to ensure that the network is not plotted outside the plotting region
high.spacing	distance between upper boxes, default is is NULL, so automatically spaced that length of upper and lower boxes is the same. Be aware if set to any value that x.lim may has to be adjusted to ensure that the network is not plotted outside the plotting region
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.high	color of upper boxes, default is grey10.
col.low	color of lower boxes, default is grey10.
bor.col.interaction	border color of interaction, default is black
bor.col.high	border color of upper boxes, default is black
bor.col.low	border color of lower boxes, default is black
high.lablength	number of characters of upper labels that should be plotted. If zero no labels are shown, default is NULL which plots the complete labels.
low.lablength	number of characters of lower 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.high and seq.low, 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	Named vector with independent abundance estimates for the lower trophic level, NULL if none exists. See Notes!
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	Named vector with independent abundance estimates for the higher trophic level, NULL if none exists. See Notes!
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
adj.high	Adjust upper labels. See adj in ?text how to adjust labels
adj.low	Adjust upper labels. See adj in ?text how to adjust labels
plot.axes	axis are plotted. Sometimes useful to place boxes in higher order plots. Defaults to FALSE
low.y	Position of the higher boxes on the y-axis. Defaults to 1.5
high.y	Position of the higher boxes on the y-axis. Defaults to 1.5
add	if set to TRUE a new bipartite network is added to the previous plot. In this way multitrophic webs can be plotted, see examples below. Defaults to FALSE.
y.lim	To set limits for y-axis. Useful if labels are plotted outside the plotting region and for multitrophic plots, see examples below
x.lim	To set limits for x-axis. Useful if labels are plotted outside the plotting region and for multitrophic plots, see examples below
low.plot	Defines if lower boxes should be drawn. Use in multitrophic plots to avoid plotting boxes of some trophic levels - see examples below. Defaults to TRUE
high.plot	Defines if higher boxes should be drawn. Use in multitrophic plots to avoid plotting boxes of some trophic levels - see examples below. Defaults to TRUE
high.xoff	allows to set an offset to upper boxes. Useful if high.spacing is used to centre boxes manually. Use plot.axes=TRUE for easy centring
low.xoff	allows to set an offset to lower boxes. Useful if low.spacing is used to centre boxes manually. Use plot.axes=TRUE for easy centring
high.lab.dis	normally labels are staggered to avoid plotting over themselves. if set to 0, higher labels are all on one horizontal line. By using ad.low the position of the labels can be adjusted. If set to any other value labels are staggered with this distance. Defaults to NULL
low.lab.dis	normally labels are staggered to avoid plotting over themselves. if set to 0, lower labels are all on one horizontal line. By using ad.low the position of the labels can be adjusted. If set to any other value labels are staggered with this distance. Defaults to NULL
abuns.type	How to plot abundances - are they independent (e.g. flower cover) measurements or are they additional (e.g. unparasitised hosts) measurements? Defaults to additional. Option none is interpreted in the same way as additional. See Notes!

Value

Returns a window with a bipartite graph of a food web. For all colours vectors can be used (which are recycled if length differs. Now more trophic webs can be plotted by using plotweb and the add switch, which allows to add more webs and staggering them on top of each other. Preferred option is here to order webs by yourself and use method="normal" to keep your preferred order. See examples on three and four trophic networks.

Note

Note that in previous implementations, low.abun and high.abun was actually treated as 'additional abundances' (e.g. unparasitised hosts). We added the parameter abuns.type to switch between the classic function (values none and additional, the default for backward compatibility) and an alternative function that plots fully independent abundance estimates (abuns.type="independent"). To change box (species) colors with abuns.type='independent', use low.abun.col and high.abun.col. The function will likely be revised again in the future, so feedback welcome.

If you have total abundance measure but want to plot used and unused resources, use abuns.type='additional' and low.abun= your.low.abun - rowSums(web).

Author(s)

Bernd Gruber [e-mail]

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 food webs see visweb

Examples

data(Safariland)
plotweb(Safariland)

# shorter labels
plotweb(Safariland, high.lablength=3, low.lablength=0, arrow="down")

# centered triangles for displaying interacions
plotweb(Safariland, text.rot=90, arrow="down.center", col.interaction="wheat2",
	y.lim=c(-1,2.5))

#orginal sequence, up arrows and different box width
plotweb(Safariland, method="normal", arrow="up", y.width.low=0.3, low.lablength=4)
# interactions as lines
plotweb(Safariland, arrow="both", y.width.low=0.05, text.rot=90, col.high="blue", 
	col.low="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.low=0.05, y.width.high=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.high=c("orange","green"))
plotweb(Safariland,col.low=c("orange","green"),col.high=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, low.lablength=10, high.lablength=5)


#example one (tritrophic)
plotweb(Safariland,y.width.low=0.1, y.width.high=0.05,method="normal", 
	y.lim=c(0,3), arrow="up", adj.high=c(0.5,1.5), col.high="orange",
	high.lablength=3,high.lab.dis=0)

plotweb(t(Safariland), y.width.low=0.05, y.width.high=0.1, method="normal",
	add=TRUE,low.y=1.5,high.y=2.5, col.low="green", text.low.col="red", 
	low.lab.dis=0, arrow="down", adj.low=c(0.5,1.1),low.plot=FALSE)

#example two (4 trophic with abundance)
low.abun = round(runif(dim(Safariland)[1],1,40)) #create
names(low.abun) <- rownames(Safariland)
plotweb(Safariland, text.rot=90, high.abun=low.abun, col.interaction="purple", 
	y.lim=c(0,4.5), high.lablength=0, arrow="up", method="normal", 
	y.width.high=0.05)

plotweb(t(Safariland), y.width.low=0.05, y.width.high=0.1, method="normal", 
	add=TRUE, low.y=1.7,high.y=2.7, col.low="green", text.low.col="black", 
	low.lab.dis=0, arrow="down", adj.low=c(0.5,1.1), low.lablength=4, 
	high.lablength=0)

plotweb(Safariland,y.width.low=0.05, y.width.high=0.1, method="normal", 
	add=TRUE, low.y=2.95, high.y=3.95, col.low="green", text.low.col="black", 
	low.lab.dis=0, arrow="down", adj.low=c(0.5,1.1), low.lablength=4)

# now some examples with the abuns.type-option:
plotweb(Safariland, abuns.type='independent',arrow="down.center")
plotweb(Safariland, abuns.type='additional',arrow="down.center")

bipartite documentation built on May 29, 2024, 2:23 a.m.