createOrderedSimMat: Update colnames and rownames of a similarity matrix according...

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

Description

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

Usage

createOrderedSimMat(similarityMatrix, order = c("retentionTime", "mz", "clustering"))

Arguments

similarityMatrix	matrix, similarityMatrix contains pair-wise similarity coefficients which give information about the similarity between precursors
order	character, one of "retentionTime", "mz" or "clustering"

Details

createOrderSimMat takes a similarity matrix 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. createOrderSimMat 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

createOrderedSimMat returns a similarity matrix with ordered rownames according to the character vector given to order

Author(s)

Thomas Naake, [e-mail]

Examples

data("binnedMSP", package = "MetCirc")
data("similarityMat", package = "MetCirc")
## order according to retention time 
createOrderedSimMat(similarityMatrix = similarityMat, order = "retentionTime")

PlantDefenseMetabolism/MetCirc documentation built on May 8, 2019, 2:52 p.m.