plotCircos {MetCirc} | R Documentation

## Circular plot to visualise similarity

### 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, thomasnaake@googlemail.com

### 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)

[Package MetCirc version 1.20.0 Index]