plotCircos {MetCirc} | R Documentation |
Circular plot to visualise similarity
plotCircos(groupname, linkDf, initialize=c(TRUE, FALSE), featureNames=c(TRUE, FALSE), cexFeatureNames=0.3, groupSector=c(TRUE, FALSE), groupName=c(TRUE, FALSE), links=c(TRUE, FALSE), highlight=c(TRUE, FALSE), colour=NULL, transparency=0.2)
groupname |
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linkDf |
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initialize |
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featureNames |
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cexFeatureNames |
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groupSector |
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groupName |
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links |
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highlight |
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colour |
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transparency |
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Internal use for shinyCircos
or used outside of
shinyCircos
to reproduce figure
The function will initialize a circlize plot and/or will plot features of a circlize plot.
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 simM <- orderSimilarityMatrix(similarityMat, spectra=spectra_tissue[1:10], type="retentionTime", ) ## create link data.frame linkDf <- createLinkDf(similarityMatrix=simM, spectra=spectra_tissue, condition=c("SPL", "LIM", "ANT", "STY"), lower=0.5, upper=1) ## cut link data.frame (here: only display links between groups) linkDf_cut <- cutLinkDf(linkDf, type="inter") ## set circlize paramters 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) ## actual plotting plotCircos(groupname, linkDf_cut, initialize=TRUE, featureNames=TRUE, cexFeatureNames=0.3, groupSector=TRUE, groupName=FALSE, links=FALSE, highlight=FALSE, colour=NULL, transparency=0.2)