plotCircos {MetCirc} | R Documentation

## Circular plot to visualise similarity

### Description

Circular plot to visualise similarity

### Usage

    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)

### 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
`linkMat` | `data.frame` containing linked features in each row, has five columns (group1, name1, group2, name2, NDP)
`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

    ## 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)

[Package MetCirc version 1.14.0 Index]