PlotTLPS {cheddar} | R Documentation

## Plot trophic-link properties

### Description

High-level functions for plotting trophic link properties.

### Usage

    PlotTLPS(community,
             X,
             Y,
             xlab,
             ylab,
             axes.limits.equal = FALSE,
             xlim = NULL,
             ylim = NULL,
             main = CPS(community)$title,
             highlight.links = NULL,
             lowlight.links = NULL,
             colour.by,
             colour.spec,
             col = NULL,
             symbol.by,
             symbol.spec,
             pch = NULL,
             bg.by,
             bg.spec,
             bg = NULL,
             cex.by = NULL,
             cex.spec = NULL,
             cex = NULL,
             are.values = FALSE,
             ...)

    PlotPredationMatrix(community,
                        xlab='Consumer',
                        ylab='Resource',
                        resource.order,
                        consumer.order,
                        ...)

    PlotMRvMC(community,
              xlab=Log10MLabel(community, name='italic(M)[consumer]'),
              ylab=Log10MLabel(community, name='italic(M)[resource]'),
              axes.limits.equal = TRUE,
              ...)

    PlotMCvMR(community,
              xlab=Log10MLabel(community, name='italic(M)[resource]'),
              ylab=Log10MLabel(community, name='italic(M)[consumer]'),
              axes.limits.equal = TRUE,
              ...)

    PlotNRvNC(community,
              xlab=Log10NLabel(community, name='italic(N)[consumer]'),
              ylab=Log10NLabel(community, name='italic(N)[resource]'),
              axes.limits.equal = TRUE,
              ...)

    PlotNCvNR(community,
              xlab=Log10NLabel(community, name='italic(N)[resource]'),
              ylab=Log10NLabel(community, name='italic(N)[consumer]'),
              axes.limits.equal = TRUE,
              ...)

    PlotBRvBC(community,
              xlab=Log10BLabel(community, name='italic(B)[consumer]'),
              ylab=Log10BLabel(community, name='italic(B)[resource]'),
              axes.limits.equal = TRUE,
              ...)

    PlotBCvBR(community,
              xlab=Log10BLabel(community, name='italic(B)[resource]'),
              ylab=Log10BLabel(community, name='italic(B)[consumer]'),
              axes.limits.equal = TRUE,
              ...)

### Arguments

`community` | an object of class `Community`.

`X`

the name of a node or link property to plot on the x axis. If the name begins with 'resource.' or 'consumer.', the remainder of the name is assumed to be a node property and should meet the criteria of the `node.properties` parameter of `TLPS`, otherwise the name is assumed to be a link property and should meet the criteria of the `link.properties` parameter of `TLPS`.

If `are.values` is `TRUE` then `X` and `Y` should be vectors of length `NumberOfTrophicLinks`.

`Y` | plotted on the y axis; see `X`.
`xlab` | title of the x axis.
`ylab` | title of the y axis.
`axes.limits.equal` | logical - if `TRUE` and `xlim` and `ylim` are `NULL` then the limits of the x and y axes will be the same.
`xlim` | limits of the x axis
`ylim` | limits of the y axis
`main` | title of the plot
`highlight.links` | trophic links to be highlighted; either `NULL`, a vector of trophic link indices or a function that takes a `Community` as its only parameter and returns a `data.frame` containing the columns ‘resource’ and ‘consumer’, which should contain node names.
`lowlight.links` | trophic links to be lowlighted; should meet criteria of `lowlight.links`.

`colour.by`

trophic link colours property. Either `NULL`, a vector of length `NumberOfTrophicLinks` or a name. If the name begins with 'resource.' or 'consumer.', the remainder of the name is assumed to be a node property and should meet the criteria of the `node.properties` parameter of `TLPS`, otherwise the name is assumed to be a link property and should meet the criteria of the `link.properties` parameter of `TLPS`.

`colour.spec` | trophic links colours specification. either `NULL` or a named vector that maps values of `colour.by` to plotting values.
`col` | trophic links colours.
`symbol.by` | trophic links symbols property; must meet the criteria of `colour.by`.
`symbol.spec` | trophic links symbols specification specification; must meet the criteria of `colour.spec`.
`pch` | trophic links symbols.
`bg.by` | trophic links background colours property; must meet the criteria of `colour.by`
`bg.spec` | trophic links background colours specification; must meet the criteria of `colour.spec`.
`bg` | trophic links background colours.
`cex.by` | trophic links cex property; must meet the criteria of `colour.by`
`cex.spec` | cex values specification; must meet the criteria of `colour.spec`.
`cex` | cex values.
`are.values` | logical - if `TRUE` `X` and `Y` must be vectors of values of length `NumberOfTrophicLinks`.
`resource.order` | the order in which to show resources. Either missing, which implies the native node order, a vector of length `NumberOfTrophicLinks` containing the integer order of resources, or the name of a property that meets the criteria of the `properties` parameter of `NPS`.
`consumer.order` | the order in which to show consumer; requirements are the same as `resource.order`.
`...` | other values to plot functions.

### Details

The general-purpose function `PlotTLPS` plots one trophic-link property against another.

If `colour.by`/`bg.by`/`symbol.by` is `NULL` and `community` has a node property named ‘category’ then trophic-link colours/background colours/symbols are given by ‘resource.category’ using `colour.spec`/`bg.spec`/`symbol.spec` given by `DefaultCategoryColours`/`DefaultCategorySymbols`.

`PlotPredationMatrix` shows trophic links as a binary matrix with species shown in node order, starting at the top-left. If `row.node` and `col.order` are both missing (the default) or are the same, then a dashed diagonal line is drawn. Points on the dashed line indicate cannibalistic trophic links.

The convenience functions `PlotMRvMC`, `PlotMCvMR`, `PlotNRvNC`, `PlotNCvNR`, `PlotBRvBC`, `PlotBCvBR` are ‘wrappers’ around `PlotRankNPS` that plot a log10-transformed body mass, M, numerical abundance, N, or biomass abundance, B.

### Author(s)

Lawrence Hudson

### See Also

`Community`, `TLPS`, `PlotBSpectrum`, `PlotCircularWeb`, `PlotNPS`, `PlotNPSDistribution`, `PlotNSpectrum`, `PlotRankNPS`, `PlotWebByLevel`

### Examples

    data(TL84)

    # The predation matrix
    PlotPredationMatrix(TL84)

    # The predation matrix with rows ordered by body mass
    PlotPredationMatrix(TL84, resource.order='M')

    # Colours and symbols by resource.category
    PlotMCvMR(TL84)

    # Colours and symbols by consumer.category
    PlotMCvMR(TL84, bg.by='consumer.category', symbol.by='consumer.category',
              colour.by='consumer.category')

    # Consumer trophic height against resource log10(M)
    PlotTLPS(TL84, 'resource.Log10M', 'consumer.TrophicHeight')

    # Log10(M of resource / M of consumer) against consumer log10(M)
    PlotTLPS(TL84, 'consumer.Log10M', 'Log10RCMRatio')

[Package cheddar version 0.1-633 Index]