highlight {MetCirc} | R Documentation

## Add links and highlight sectors

### Description

A function to add links and highlight sectors to an initialised and plotted `circlize` plot with one track.

### Usage

    highlight(groupname, ind, linkDf, colour=NULL, transparency=0.4, links=TRUE)

### Arguments

`groupname` | `character` vector containing "group" and "name" to display, that is a unique identifier of the features, "group" and "name" have to be separated by `"_"` where "group" is the first and "name" is the last element
`ind` | `numeric`, indices which will be highlighted
`linkDf` | `data.frame`, in each row there is information about features to be connected
`colour` | `NULL` or `character`, colour defines the colours which are used for plotting, if `NULL` default colours are used
`transparency` | `numeric`, defines the transparency of the colours
`links` | `logical`, should links of unselected features be plotted

### Details

Internal use for `shinyCircos` or outside of `shinyCircos` to reproduce the figure.

### Value

The function will update an existing plot by highlighting a specified sector and connected links.

### Author(s)

Thomas Naake, thomasnaake@googlemail.com

### Examples

    data("spectra", package="MetCirc")
    similarityMat <- compare_Spectra(spectra_tissue[1:10],
        fun=normalizeddotproduct, binSize=0.01)
     ## order similarityMat according to retentionTime and update rownames
     simM <- orderSimilarityMatrix(similarityMat, spectra=spectra_tissue[1:10],
                 type="retentionTime")
     ## create link matrix
     linkDf <- createLinkDf(similarityMatrix=simM, spectra=spectra_tissue,
         condition=c("SPL", "LIM", "ANT", "STY"), lower=0.5, upper=1)
     ## cut link matrix (here: only display links between groups)
     linkDf_cut <- cutLinkDf(linkDf, type="inter")
     ## set circlize parameters
     circos.par(gap.degree=0, cell.padding=c(0.0, 0, 0.0, 0),
             track.margin=c(0.0, 0))
     groupname <- c(as.character(linkDf_cut[, "spectrum1"]),
                     as.character(linkDf_cut[, "spectrum2"]))
     groupname <- unique(groupname)
     ## here: set indSelected arbitrarily
     indSelected <- c(2,3)
     ## actual plotting
     plotCircos(groupname, linkDf_cut, initialize=TRUE,
         featureNames=TRUE, cexFeatureNames=0.2, groupSector=TRUE,
         groupName=FALSE, links=FALSE, highlight=TRUE)
     ## highlight
     highlight(groupname=groupname, ind=indSelected, linkDf=linkDf_cut,
         colour=NULL, transparency=0.4, links=TRUE)

[Package MetCirc version 1.18.0 Index]