circosLegend: Plot a legend for circos plot

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

Plot a legend for circos plot

Description

circosLegend plots a legend for circos plot using group names.

Usage

circosLegend(groupname, highlight = TRUE, colour = NULL, cex = 1)

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
highlight	logical, should colours be adjusted to highlight settings?
colour	NULL or character, colour defines the colours which are used for plotting, if NULL default colours are used
cex	numeric, parameter that controls size of the legend in the plot

Details

Internal use in shinyCircos or outside of shinyCircos to reproduce figures.

Value

The function will open a new plot and display colours together with labels.

Author(s)

Thomas Naake, [e-mail]

Examples

data("spectra", package = "MetCirc")

## create similarity matrix
similarityMat <- Spectra::compareSpectra(sps_tissue[1:10],
    FUN = MsCoreUtils::ndotproduct, ppm = 20, m = 0.5, n = 2)
rownames(similarityMat) <- colnames(similarityMat) <- sps_tissue$name[1:10]

linkDf <- createLinkDf(similarityMatrix = similarityMat,
    sps = sps_tissue[1:10],
    condition = c("SPL", "LIM", "ANT", "STY"), lower = 0.01, upper = 1)

## cut link data.frame (here: only display links between groups)
linkDf_cut <- cutLinkDf(linkDf, type = "inter")
groupname <- c(as.character(linkDf_cut[, "spectrum1"]),
            as.character(linkDf_cut[, "spectrum2"]))
groupname <- unique(groupname)

## plot legend
circosLegend(groupname, highlight = TRUE, colour = NULL, cex = 1)

tnaake/MetCirc documentation built on Dec. 7, 2022, 7:42 a.m.