addLink {combi} | R Documentation

## Add a link on a compositional plot

### Description

Add a link on a compositional plot

### Usage

    addLink(DIplot, links, Views, samples, variable = NULL, Dims = c(1, 2),
      addLabel = FALSE, labPos = NULL, projColour = "grey",
      latentSize = 0.25)

### Arguments

`DIplot` | A list with ggplot object where the links are to be added, and data frames with coordinates (obtained by setting plot(..., returnCoords = TRUE))
`links` | A matrix containing either feature names (two column matrix) or approximate coordinates (four column matrix)
`Views` | Indices or names of the views for which the links should be added
`samples` | Sample names or approximate sample coordinates
`variable` | Name of variable in environmental gradient for which link should be plotted
`Dims` | vector of length 2 referring to the model dimensions
`addLabel` | A boolean, should arrow with label be plotted?
`labPos` | The position of the label, as a numeric vector of length 2
`projColour` | The colour of the projection, as character string
`latentSize` | Size of the line from the origin to the latent variable dot

### Value

A ggplot object with the links added

### Examples

    data(Zhang)

    #Unconstrained
    microMetaboInt = combi(
    list("microbiome" = zhangMicrobio, "metabolomics" = zhangMetabo),
    distributions = c("quasi", "gaussian"), compositional = c(TRUE, FALSE),
    logTransformGaussian = FALSE, verbose = TRUE)

    load(system.file("extdata", "zhangFits.RData", package = "combi"))
    Plot = plot(microMetaboInt, samDf = zhangMetavars, samCol = "ABX",
     returnCoords = TRUE)
    addLink(Plot, links = cbind("OTU0565b3","OTUa14fb5"), Views = 1,
     samples = c(1,1))

[Package combi version 0.99.15 Index]