highlight {MetCirc} | R Documentation |
A function to add links and highlight sectors to an initialised
and plotted circlize
plot with one track.
highlight(groupname, ind, linkDf, colour=NULL, transparency=0.4, links=TRUE)
groupname |
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ind |
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linkDf |
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colour |
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transparency |
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links |
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Internal use for shinyCircos
or outside of shinyCircos
to reproduce the figure.
The function will update an existing plot by highlighting a specified sector and connected links.
Thomas Naake, thomasnaake@googlemail.com
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)