orderSimilarityMatrix: Order columns and rows of a similarity matrix according to...

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

Order columns and rows of a similarity matrix according to m/z, retention time and clustering

Description

Internal function for shiny application. May also be used outside of shiny to reconstruct figures.

Usage

orderSimilarityMatrix(
  similarityMatrix,
  sps,
  type = c("retentionTime", "mz", "clustering"),
  group = FALSE
)

Arguments

similarityMatrix	matrix, similarityMatrix contains pair-wise similarity coefficients which give information about the similarity between precursors
sps	Spectra object containing spectra that are compared in similarityMatrix
type	character(1), one of "retentionTime", "mz", or "clustering"
group	logical(1), if TRUE group separated by "_" will be cleaved from rownames/colnames of similarityMatrix and matched against names of sps (sps$name), if FALSE rownames/colnames of similarityMatrix are taken as are and matched against names of sps (sps$name)

Details

orderSimilarityMatrix takes a similarity matrix, Spectra object (sps, containing information on m/z and retention time), and a character vector as arguments. It will then reorder rows and columns of the similarityMatrix object such, that it orders rows and columns of similarityMatrix according to m/z, retention time or clustering in each group.

orderSimilarityMatrix is employed in the shinyCircos function to create similarityMatrix objects which will allow to switch between different types of ordering in between groups (sectors) in the circos plot. It may be used as well externally, to reproduce plots outside of the reactive environment (see vignette for a workflow).

Value

matrix, orderSimilarityMatrix returns a similarity matrix with ordered rownames according to the character vector type

Author(s)

Thomas Naake, [e-mail]

Examples

data("spectra", package = "MetCirc")
similarityMat <- Spectra::compareSpectra(sps_tissue[1:10], 
    FUN = MsCoreUtils::ndotproduct, ppm = 10)
rownames(similarityMat) <- colnames(similarityMat) <- sps_tissue$name[1:10]

## order according to retention time 
orderSimilarityMatrix(similarityMatrix = similarityMat, 
    sps = sps_tissue, type = "retentionTime", group = FALSE)
    

tnaake/MetCirc documentation built on Nov. 3, 2024, 11:16 a.m.