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.clear()
     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 1.24.0 Index]