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 1.17.0 Index]