Description Usage Arguments Details Value Author(s) Examples
Circular plot to visualise similarity
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groupname |
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linkMat |
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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
1 2 3 4 5 6 7 8 9 10 11 12 13 14 15 16 17 18 19 20 21 | ## 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
simM <- createOrderedSimMat(similarityMat, order = "retentionTime")
## create link matrix
linkMat <- createLinkMatrix(similarityMatrix = simM,
threshold_low=0.8, threshold_high=1)
## cut link matrix (here: only display links between groups)
linkMat_cut <- cutLinkMatrix(linkMat, 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 <- rownames(simM)
## actual plotting
plotCircos(groupname, linkMat_cut, initialize = TRUE,
featureNames = TRUE, cexFeatureNames = 0.3, groupSector = TRUE,
groupName = FALSE, links = FALSE, highlight = FALSE, colour = NULL,
transparency = 0.2)
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