Converts a Cardinal Object into a SpaMTP Seurat Object

Converts a Cardinal Object into a SpaMTP Seurat Object

Usage

CardinalToSeurat(
  data,
  multi.run = FALSE,
  seurat.coord = NULL,
  assay = "Spatial",
  verbose = TRUE
)

Arguments

data

A Cardinal Object that is being converted into a Seurat Object.

multi.run

Boolean indicating if there are multiple runs within the imported data. If TRUE, an index will be added to the pixel names per run, and an individual FOV will be generated per run in the Seurat Object (default = FALSE).

seurat.coord

A Data.Frame containing two columns titled 'X_new' and 'Y_new' specifying the pixel coordinates of each data point. This is only required if mapping Spatial Metabolic data with a H&E image was done externally, and the SM coordinates need to change to align correctly to the ST data. Else, set to NULL (default = NULL).

assay

Character string containing the name of the assay (default = "Spatial").

verbose

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

Value

A Seurat Object containing the mz count data of the supplied Cardinal Object

Examples

# CardinalToSeurat(CardinalObj, run_name = "run_1", seurat.coord = NULL)