networkplot: Correlation network from spectral similarity data
In CluMSID: Clustering of MS2 Spectra for Metabolite Identification

Description Usage Arguments Value Examples

networkplot() is used to generate correlation networks from spectral similarity data. An interactive visualisation can be produced using plotly.

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networkplot(distmat, interactive = FALSE, show_labels = FALSE,
    label_size = 1.5, highlight_annotated = FALSE,
    min_similarity = 0.1, exclude_singletons = FALSE)

`distmat`	A distance matrix as generated by `distanceMatrix`.
`interactive`	Logical, defaults to `FALSE`. If `TRUE`, an interactive visualisation is generated using plotly.
`show_labels`	Logical, defaults to `FALSE`. If `TRUE`, feature IDs are printed as labels in the network plot. Argument has no effect if `interactive` is `TRUE` (because in this case, labels are displayed on mouse-over).
`label_size`	Numeric, defaults to `1.5`. If `show_labels` is `TRUE` and `interactive` is `FALSE`, `label_size` defines the size of labels in the plot.
`highlight_annotated`	Logical, defaults to `FALSE`. If `TRUE`, points for features for which an annotation was added before using `distanceMatrix` are highlighted by red colour, while other points are grey in the network plot.
`min_similarity`	Numeric, defaults to `0.1`. The minimum spectral contrast angle (see`cossim`) that is considered a spectral similarity and hence a connection in the network.
`exclude_singletons`	Logical, defaults to `FALSE`. If `TRUE`, features that have no connection to any other feature will not be displayed in the network plot.

A network plot generated with the help of network, ggnet2 and, if interactive, ggplotly. Edge weights correspond to spectral similarities.

load(file = system.file("extdata",
    "distmat.RData",
    package = "CluMSIDdata"))

networkplot(distmat[1:50,1:50], show_labels = TRUE,
                exclude_singletons = TRUE)