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 1.17.0 Index]