Saves SpaMTP Object

This function saves a SpaMTP Seurat Object into a standard single-cell/spatial file format. This includes a filtered_feature_bc_matrix folder containing files storing the features, barcode/pixels and intensity matrix. Metadata and sapatial files (such as scale factors and hires/lowres images) are also stored.

Usage

SaveSpaMTPData(
  data,
  outdir,
  assay = "Spatial",
  slot = "counts",
  image = NULL,
  annotations = FALSE,
  verbose = TRUE
)

Arguments

data

A Spatial Metabolomic SpaMTP Seurat Object being saved.

outdir

Character string of the directory to save the mtx.mtx, barcode.tsv, features.tsv, barcode_metadata.csv and feature_metadata.csv in.

assay

Character string defining the Seurat assay that contains the m/z count data (default = "Spatial").

slot

Character string defining the Seurat assay slot that contains the m/z values directly (default = "counts").

image

Character string defining the image stored within the SpaMTP Seurat object to save. If NULL no image will be saved (default = NULL).

annotations

Boolean values defining if the Seurat Object contains annotations to be saved (default = FALSE).

verbose

Boolean indicating whether to show informative processing messages. If TRUE the message will be show, else the message will be suppressed (default = TRUE).

Details

• This can be used for saving data for transfer to python. Can be read in as Anndata using scanpy.read_10x_mtx().

• For saving in R saveRDS() is recommended.

Examples

# saveSpaMTPData(SeuratObject, "../output", annotations = TRUE)