bipartite: plotModuleWeb – R documentation

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plotModuleWeb

Description

This function takes an object of class moduleWeb and plots the modules found by function computeModules(...) onto the graph.

Usage

plotModuleWeb(moduleWebObject, plotModules = TRUE, 
rank = FALSE, weighted = TRUE, displayAlabels = TRUE, 
displayBlabels = TRUE, labsize = 1, xlabel = "", ylabel = "", 
square.border = "white", fromDepth = 0, upToDepth = -1)

Arguments

`moduleWebObject`	An object of class "moduleWeb".
`plotModules`	If `plotModules` is true, modules are plotted onto the graph, otherwise only the graph itself is plotted.
`rank`	logical; if true, rows will be standardised for plotting, yielding a range from light to dark blue for each row; if false, values are ranged across the entire matrix. The latter is more faithful to the data, while the former makes lower levels more comparable, irrespective of marginal totals.
`weighted`	If `weighted` is true, the intensity of squares representing the edges corresponds with the edge weight, otherwise all squares representing existing edges have equal intensity.
`displayAlabels`	Row labels are plotted, iff `displayAlabels` is true.
`displayBlabels`	Column labels are plotted, iff `displayBlabels` is true.
`labsize`	`labsize` is the scalar factor with which the size of the plot labels can be changed.
`xlabel`	`xlabel` is the label for the x-axis.
`ylabel`	`ylabel` is the label for the y-axis.
`square.border`	Background color of area with squares.
`fromDepth`	Minimal depth of modules which should be plotted.
`upToDepth`	Maximal depth of modules which should be plotted. If upToDepth is smaller then fromDepth, all modules are plotted.

Value

A plot window with appropriate size according to the dimensions of the web.

Author(s)

Rouven Strauss

Examples

## Not run: 
data(small1976)

moduleWebObject = computeModules(small1976);
plotModuleWeb(moduleWebObject);

## End(Not run)

bipartite

Visualising Bipartite Networks and Calculating Some (Ecological) Indices

v2.16

GPL

Authors

Carsten F. Dormann, Jochen Fruend and Bernd Gruber, with additional code from Stephen Beckett, Mariano Devoto, Gabriel Felix, Jose Iriondo, Tove Opsahl, Rafael Pinheiro, Rouven Strauss and Diego Vazquez, also based on C-code developed by Nils Bluethgen, Aaron Clauset/Rouven Strauss and Miguel Rodriguez-Girones

Initial release

2021-02-08