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.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 1.18.0 Index]