printInformationSelect: Display information on connected features of selected...

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

Description

Displays information on connected features of selected features.

Usage

printInformationSelect(
  select,
  spectra = NULL,
  linkDfInd,
  linkDf,
  similarityMatrix,
  roundDigits = 2
)

Arguments

select	'character', obtained from groupname, 'character' of selected feature
spectra	'MSpectra' object containing spectra that are compared in 'similarityMatrix'
linkDfInd	'numeric' indices of selected features
linkDf	'data.frame' that contains information of linked features for given thresholds
similarityMatrix	'matrix' that is used to get information on the degree of similarity, 'similarityMat' is an ordered version of a similarity matrix, see '?orderSimilarityMatrix'
roundDigits	'numeric', how many digits should be displayed?

Details

'printInformationSelect' is for internal use.

Value

'character' that is in HTML format

Author(s)

Thomas Naake, [e-mail]

Examples

data("spectra", package = "MetCirc")
similarityMat <- compare_Spectra(spectra_tissue[1:10],
    fun = normalizeddotproduct, binSize = 0.01)
linkDf <- createLinkDf(similarityMatrix = similarityMat,
    spectra = spectra_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)
## arbitrarily select a feature
ind <- 2
linkDfInds <- getLinkDfIndices(groupname[ind], linkDf_cut)
MetCirc:::printInformationSelect(groupname[ind], 
    spectra = spectra_tissue[1:10], linkDfInd = linkDfInds, 
    linkDf = linkDf_cut, similarityMatrix = similarityMat)

MetCirc documentation built on Nov. 8, 2020, 8:26 p.m.