Generates interactive 3D spatial density plot for m/z values
Source:R/PlottingSpaMTP.R
DensityMap.RdThis 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()