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 |
'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 |
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.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)