Format a cellprofiler image into a SpatialExperiment object — format_cellprofiler_to

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()` Note that if the data does not include these parameters, we recommend adding it to the output from cellprofiler with NAs in columns.

format_cellprofiler_to_spe(
  path = NULL,
  markers = NULL,
  intensity_columns_interest = NULL
)

Arguments

path: String of the path location cellprofiler csv file.
markers: String Vector containing the markers used for staining.
intensity_columns_interest: String Vector with the names of the columns with the level of each marker. Column names must match the order of the 'markers' parameter.

Value

A SpatialExperiment object is returned

Details

Note when specifying `markers`, please use "DAPI" to replace "DNA" due to implementation. The output data will include "DAPI" instead of "DNA".

Examples

path <- system.file("extdata", "tiny_cellprofiler.txt.gz", package = "SPIAT")
markers <- c("Marker1", "Marker2", "Marker3", "Marker4", "Marker5", "DAPI", 
"Marker6")
intensity_columns_interest <- c("Intensity_MeanIntensity_Marker1_rs",
"Intensity_MeanIntensity_Marker2_rs", "Intensity_MeanIntensity_Marker3_rs",
"Intensity_MeanIntensity_Marker4_rs", "Intensity_MeanIntensity_Marker5_rs",
"Intensity_MeanIntensity_DAPI_rs", "Intensity_MeanIntensity_Marker6_rs")
formatted_cellprofiler <- format_cellprofiler_to_spe(path = path,
markers = markers, intensity_columns_interest = intensity_columns_interest)