Read Spatial Metabolomics matrix file (.csv format)

This function reads in SM data stored in a table format. This table must contain two rows named 'x' and 'y' storing the respective pixel coordinates. All other columns should be the relative m/z values containing the intensity values of each pixel.

Usage

ReadSM_mtx(
  mtx.file,
  assay = "Spatial",
  verbose = TRUE,
  feature.start.column = 1,
  mz.prefix = NULL,
  project.name = "SpaMTP"
)

Arguments

mtx.file

Character string defining the path of the spatial metabolomic image matrix .csv file.

assay

Character string of the Seurat object assay name to store the relative intensity data (default = "Spatial").

verbose

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

feature.start.column

Numeric value defining the start index containing the x, y, and m/z value columns within the table (default = 1).

mz.prefix

Character string matching the prefix string in front of each m/z name (default = NULL).

project.name

Character string defining the name of the sample to be assigned as orig.ident (default = "SpaMTP").

Value

A SpaMTP Seurat class object containing the intensity values in the counts slot of the designated assay.

Details

NOTE: The input file must be in a format similar to the table below:

A data.frame: 5 × 5
   x   y   mz1  mz2  mz3
1  0   1    0    0   11
2  0   2    0    0    0
3  0   3    0    0    0
4  0   4   20    0    0
5  0   5    0    0    0

• The first two columns (x, y) contain the respective spatial coordinates.

• The subsequent columns contain the m/z values and their intensities for each spatial pixel.

Examples

# msi_data <- ReadSM_mtx("~/Documents/msi_mtx.csv")