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

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

Display information on connected features of selected features

Description

Displays information on connected features of selected features.

Usage

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

Arguments

select	character, obtained from groupname, character of selected feature
sps	Spectra 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, similarityMatrix is an ordered version of a similarity matrix, see ?orderSimilarityMatrix
roundDigits	numeric(1), 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")
sps_tissue@metadata$names <- rep("Unknown", 259)
sps_tissue@metadata$information <- rep("Unknown", 259)
sps_tissue@metadata$classes <- rep("Unknown", 259)
sps_tissue@metadata$adduct <- rep("Unknown", 259)
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)

## arbitrarily select a feature
ind <- 2
linkDfInds <- getLinkDfIndices(groupname[ind], linkDf_cut)
MetCirc:::printInformationSelect(select = groupname[ind], 
    sps = sps_tissue[1:10], linkDfInd = linkDfInds, 
    linkDf = linkDf_cut, similarityMatrix = similarityMat)

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