Format a CODEX image into a SpatialExperiment object

Source: R/format_codex_to_spe.R

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.

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)