plotCircos {MetCirc} | R Documentation |
Circular plot to visualise similarity
plotCircos(groupname, linkMat, 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 |
|
linkMat |
|
initialize |
|
featureNames |
|
cexFeatureNames |
|
groupSector |
|
groupName |
|
links |
|
highlight |
|
colour |
|
transparency |
|
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
## 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)