format_codex_to_spe: Format a CODEX image into a SpatialExperiment object

In TrigosTeam/SPIAT: Spatial Image Analysis of Tissues

Format a CODEX image into a SpatialExperiment object

Description

Reads in spatial data in the form of cell coordinates, cell phenotypes (if available), and marker intensities and transforms to a 'SpatialExperiment' object. The assay stores the intensity level of every marker (rows) for every cell (columns). Cell phenotype is stored under colData. Cell x and y coordinates are stored under 'spatialCoords()' field.

Usage

format_codex_to_spe(path = NULL, markers, path_to_codex_cell_phenotypes = NULL)

Arguments

path	String of the path location of CODEX csv file.
markers	String Vector containing the markers used for staining.
path_to_codex_cell_phenotypes	String of the path to the Cluster ID/Cell type file.

Value

A SpatialExperiment object is returned

Examples

path <- system.file("extdata", "tiny_codex.csv.gz", package = "SPIAT")
path_to_codex_cell_phenotypes <- system.file("extdata", 
"tiny_codex_phenotypes.txt.gz", package = "SPIAT")
markers <- c("CD45", "Ly6C", "CD27", "CD5", "CD79b")
formatted_codex <- format_codex_to_spe(path = path, markers = markers,
path_to_codex_cell_phenotypes = path_to_codex_cell_phenotypes)

TrigosTeam/SPIAT documentation built on April 11, 2025, 10:02 p.m.