Generates interactive 3D spatial density plot for m/z values

This function generates an interactive HTML file that can be used to generate spatial density kernals based on the intensity of any selected m/z value.

Usage

DensityMap(object, assay = "SPM", slot = "counts", folder = getwd(), ...)

Arguments

object: SpaMTP Seurat object contains spatial metabolomics data
assay: Character string defining the Seurat assay that contains intensity values to plot (default = "SPM").
slot: Character string defining the assay slot to extract the intensity values from (default = "counts").
folder: Character string defining the directory path to save the density map HTML file to (default = getwd()).
...: Arguments passed to SpaMTP::AnnotateSeuratMALDI()

Value

Return a html contains the annotation/average intensity of peakbins/density of distribution of each peak

Examples

utils::str(formals(DensityMap))
#> Dotted pair list of 5
#>  $ object: symbol 
#>  $ assay : chr "SPM"
#>  $ slot  : chr "counts"
#>  $ folder: language getwd()
#>  $ ...   : symbol 
# DensityMap(SpaMTP.obj)