Visualise the similarity of MS/MS features in a reactive
Details the vignette for further descriptions on how to
shinyCircos(similarityMatrix, sps, condition, ...)
further arguments passed to
The function is based on the
The user can choose interactively thresholds, type of links (between or
within groups), display information about MS/MS features, permanently select
MS/MS features and export selected precursors. The
stores annotation information about the MS/MS features. Names of features
similarityMatrix have to be found as entries
sps$name are used as identifiers and
similarityMatrix are cleaved
by the group identifier (separated by
"_"). Annotation information
is taken from
spectra from the columns "names", "information",
"classes" and "adduct" in the slot
After exiting the application, the annotation will be written to the
respective columns in the slot
metadata. If one or several of these
columns is already present in
metadata, the column(s) will be used as
the source of annotation information.
shinyCircos returns a
vector with the permanently selected precursors and an object with the
MSpectra object containing the annotation.
Thomas Naake, firstname.lastname@example.org
data("spectra", package = "MetCirc") similarityMat <- Spectra::compareSpectra(sps_tissue[1:10], FUN = MsCoreUtils::ndotproduct, ppm = 10, m = 0.5, n = 2) rownames(similarityMat) <- colnames(similarityMat) <- sps_tissue$name[1:10] ## Not run: shinyCircos(similarityMatrix = similarityMat, sps = sps_tissue, condition = c("SPL", "LIM", "ANT", "STY")) ## End(Not run)
Add the following code to your website.
For more information on customizing the embed code, read Embedding Snippets.