Get relevant fields and file paths for transcript spots — getTechTxFields • SpatialFeatureExperiment

Get column names for x, y, and z coordinates, gene IDs, and cell IDs from the transcript file and get file paths for transcript spot coordinates given technology.

Usage

getTechTxFields(tech, data_dir = NULL)

Arguments

tech: Name of the commercial technology, must be one of Vizgen, Xenium, and CosMX.
data_dir: Top level directory of the output.

Value

A named list with elements:

spatialCoordsNames: A character vector for column names for the xyz coordinates of the transcript spots.
gene_col: Column name for gene IDs.
cell_col: Column name for cell IDs.
fn: File path of the transcript spot file.