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, LinkMatrix, colour = NULL, transparency = 0.4, links = TRUE)
groupname |
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ind |
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LinkMatrix |
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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
## 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)