SpatialExperimentR/add_array_coords.R
add_array_coords.RdGiven a SpatialExperiment, sample information, and coordinates
produced from the refinement workflow, add array and pixel coordinates
appropriate for the linearly transformed capture areas making up each group
present in the SpatialExperiment.
add_array_coords(spe, sample_info, coords_dir, overwrite = TRUE)A SpatialExperiment
A tibble with columns capture_area and
group
A character(1) vector giving the directory
containing sample directories each with tissue_positions.csv,
scalefactors_json.json, and tissue_lowres_image.png files
produced from refinement with prep_imagej_*() functions
A logical(1) vector indicating whether to overwrite
spatialCoords(spe), and colData(spe) columns array_row,
array_col, pixel_row_in_fullres, and
pixel_col_in_fullres with the transformed values. Note that the
original values are preserved even when TRUE, in versions of
colData(spe) columns ending in _original.
A SpatialExperiment object with additional colData
columns pxl_row_in_fullres_[suffix] and pxl_col_in_fullres_[suffix]
with [suffix] values original, transformed, and
rounded; array_row_[suffix] and array_col_[suffix]
columns with [suffix] values original and transformed; and,
if overwrite, modified colData columns array_row and
array_col and spatialCoords() with their transformed values
Array coordinates are determined via an algorithm that fits each spot to
the nearest spot on a new, imaginary, Visium-like capture area. The imaginary
capture area differs from a real capture area only in its extent; array
coordinates still start at 0 but may extend arbitrarily beyond the normal
maximum indices of 77 and 127 to fit every capture area in each group
defined in the SpatialExperiment. The goal is to return well-defined
array coordinates in a consistent spatial orientation for each group, such
that downstream applications, such as clustering with BayesSpace, can
process each group as if it really were one capture area in the first place.
# For internal testing
if (FALSE) { # \dontrun{
library("HDF5Array")
spe <- loadHDF5SummarizedExperiment("dev/test_data/spe_filtered")
sample_info <- readr::read_csv("dev/test_data/sample_info.csv")
coords_dir <- "dev/test_data"
spe_new <- add_array_coords(spe, sample_info, coords_dir, overwrite = TRUE)
} # }
## TODO: add working examples
args(add_array_coords)
#> function (spe, sample_info, coords_dir, overwrite = TRUE)
#> NULL