Format a HALO image into a SpatialExperiment object

Source: R/format_HALO_to_spe.R

Reads in HALO 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 x and y coordinates are stored under `spatialCoords()`. Cell phenotype and other cell properties are stored under colData. The cell properties to be included are Cell.Area, Nucleus.Area and Cytoplasm.Area. Note that if the data does not include these parameters, we recommend adding it to the output from HALO with NAs in columns.

format_halo_to_spe(
  path = NULL,
  markers = NULL,
  locations = NULL,
  dye_columns_interest = NULL,
  intensity_columns_interest = NULL
)

Arguments

path

String of the path location of HALO text file.

markers

String Vector containing the markers used for staining.

locations

(Optional) Vector containing the locations of markers used for staining. Location can be either "Nucleus", "Cytoplasm" or "Membrane". This is used to select the Intensity column and can be used instead of `intensity_columns_interest`.

dye_columns_interest

(Optional) Use if locations is not specified. Vector of names of the columns with the marker status (i.e. those indicating 1 or 0 for whether the cell is positive or negative for the marker). Column names must match the order of the 'markers' parameter.

intensity_columns_interest

(Optional) Use if locations is not specified. 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

Examples

raw_halo_data <- system.file("extdata", "tiny_halo.csv.gz", package="SPIAT")
markers <- c("DAPI", "CD3", "PDL-1", "CD4", "CD8", "AMACR")
intensity_columns_interest <- c("Dye 1 Nucleus Intensity",
"Dye 2 Cytoplasm Intensity","Dye 3 Membrane Intensity",
"Dye 4 Cytoplasm Intensity", "Dye 5 Cytoplasm Intensity",
"Dye 6 Cytoplasm Intensity")
dye_columns_interest <-c("Dye 1 Positive Nucleus","Dye 2 Positive Cytoplasm",
"Dye 3 Positive Membrane", "Dye 4 Positive Cytoplasm",
"Dye 5 Positive Cytoplasm", "Dye 6 Positive Cytoplasm")
formatted_HALO <- format_halo_to_spe(path=raw_halo_data,markers=markers, 
intensity_columns_interest=intensity_columns_interest,
dye_columns_interest=dye_columns_interest)
#> Rows: 10 Columns: 71
#> ── Column specification ────────────────────────────────────────────────────────
#> Delimiter: ","
#> chr  (3): Analysis Region, Analysis Inputs, Classifier Label
#> dbl (65): Object Id, XMin, XMax, YMin, YMax, Dye 1 Positive, Dye 1 Positive ...
#> lgl  (3): Image Location, Region Area (μm²), Region Perimeter (μm)
#> 
#> ℹ Use `spec()` to retrieve the full column specification for this data.
#> ℹ Specify the column types or set `show_col_types = FALSE` to quiet this message.