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

Description Usage Arguments Details Value Author(s) Examples

Description

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

Usage

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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, thomasnaake@googlemail.com

Examples

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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.