minFragCart2Polar: Calculate the nearest feature in polar coordinates given...

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

Calculate the nearest feature in polar coordinates given cartesian coordinates

Description

Calculates the nearest feature in polar coordinates given cartesian coordinates.

Usage

minFragCart2Polar(x, y, degreeOfFeatures)

Arguments

x	numeric, cartesian x coordinate
y	numeric, cartesian y coordinate
degreeOfFeatures	list of positions of features

Details

minFragCart2Polar is employed to find the feature with the smallest distance from given cartesian coordinates.

Value

minFragCart2Polar returns the index of the feature that has the smallest distance to the given coordinates. As minFragCart2Polar is used in shinyCircos for the track 1 only polar r coordinates between 0.8 and 1 will be used to find the feature with smallest distance.

Author(s)

Thomas Naake, [e-mail]

Examples

library("MsCoreUtils")
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 = 0.5, 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)

## set circlize parameters
circos.clear()
circos.par(gap.degree = 0, cell.padding = c(0.0, 0, 0.0, 0),
    track.margin = c(0.0, 0))
plotCircos(groupname, NULL, initialize = TRUE, featureNames = FALSE,
    groupName = FALSE, groupSector = FALSE, links = FALSE, highlight = FALSE)
x <- 1
y <- 0
degreeFeatures <- lapply(groupname,
    function(x) 
        mean(circlize:::get.sector.data(x)[c("start.degree", "end.degree")]))
minFragCart2Polar(x, y, degreeOfFeatures = degreeFeatures)

tnaake/MetCirc documentation built on April 23, 2023, 8:56 a.m.