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, LinkMatrix, 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
`LinkMatrix` | `matrix`, 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

     ## load binnedMSP
     data("binnedMSP", package = "MetCirc")
     ## use only a selection
     binnedMSP <- binnedMSP[c(1:20, 29:48, 113:132, 240:259),]
     similarityMat <- createSimilarityMatrix(binnedMSP)
     ## order similarityMat according to retentionTime and update rownames
     simM <- createOrderedSimMat(similarityMat, order = "retentionTime")
     ## create link matrix
     linkMat <- createLinkMatrix(similarityMatrix = simM,
         threshold_low = 0.95, threshold_high = 1)
     ## cut link matrix (here: only display links between groups)
     linkMat_cut <- cutLinkMatrix(linkMat, 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 <- rownames(simM)
     ## here: set selectedFeatures arbitrarily
     indSelected <- c(2,23,42,62)
     selectedFeatures <- groupname[indSelected]
     ## actual plotting
     plotCircos(groupname, linkMat_cut, initialize = TRUE,
         featureNames = TRUE, cexFeatureNames = 0.2, groupSector = TRUE,
         groupName = FALSE, links = FALSE, highlight = TRUE)
     ## highlight
     highlight(groupname = groupname, ind = indSelected, LinkMatrix =
             linkMat_cut, colour = NULL, transparency = 0.4, links = TRUE)

[Package MetCirc version 1.10.0 Index]