highlight: Add links and highlight sectors

In PlantDefenseMetabolism/MetCirc: Navigating mass spectral similarity in high-resolution MS/MS metabolomics data

Description

A function to add links and highlight sectors to an initialised and plotted circlize plot with one track.

Usage

highlight(groupname, ind, LinkMatrix, colour = NULL, transparency = 0.4, links = TRUE)

Arguments

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
LinkMatrix	matrix, 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

Details

Internal use for shinyCircos or outside of shinyCircos to reproduce the figure.

Value

The function will update an existing plot by highlighting a specified sector and connected links.

Author(s)

Thomas Naake, [e-mail]

Examples

 ## 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)

PlantDefenseMetabolism/MetCirc documentation built on May 8, 2019, 2:52 p.m.