plotCircos: Circular plot to visualise similarity

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

Description

Circular plot to visualise similarity.

Usage

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
)

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
linkDf	'data.frame' containing linked features in each row, has five columns (group1, spectrum1, group2, spectrum2, similarity)
initialize	'logical', should plot be initialized?
featureNames	'logical', should feature names be displayed?
cexFeatureNames	'numeric' size of feature names
groupSector	'logical', should groups be displayed with background colours?
groupName	'logical', should group names (e.g. compartment names or individual names) be displayed?
links	'logical', should links be plotted?
highlight	'logical', highlight is set to 'TRUE'
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

Details

Internal use for 'shinyCircos' or used outside of 'shinyCircos' to reproduce figure

Value

The function will initialize a circlize plot and/or will plot features of a circlize plot.

Author(s)

Thomas Naake, [e-mail]

Examples

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.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)
## 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)

MetCirc documentation built on Nov. 8, 2020, 8:26 p.m.