Add a function for building the full SpatialExperiment object from Sa…

…mui outputs

NAMESPACE

@@ -2,6 +2,7 @@
 
 export(add_array_coords)
 export(add_overlap_info)
+export(build_spe)
 export(spe_to_seurat)
 export(spot_plot)
 import(Seurat)
@@ -12,6 +13,7 @@ import(spatialLIBD)
 import(tibble)
 importFrom(S4Vectors,DataFrame)
 importFrom(SummarizedExperiment,colData)
+importFrom(dplyr,as_tibble)
 importFrom(dplyr,filter)
 importFrom(dplyr,mutate)
 importFrom(dplyr,pull)

R/build_spe.R

@@ -0,0 +1,87 @@
+#' Build stitched \code{SpatialExperiment}
+#'
+#' First, read in capture-area-level spaceranger outputs. Then, overwrite
+#' spatial coordinates and images to represent group-level samples using
+#' \code{sample_info$group} (though keep original coordinates in
+#' \code{colData} columns ending in "_original"). Next, add info about
+#' overlaps (via \code{spe$exclude_overlapping} and \code{spe$overlap_key}).
+#' Ultimately, return a \code{SpatialExperiment} ready for visualization or
+#' downstream analysis.
+#'
+#' @inheritParams add_array_coords
+#' @inheritParams add_overlap_info
+#' @param count_type A \code{character(1)} vector passed to \code{type} from
+#' \code{SpatialExperiment::read10xVisium}, defaulting to "sparse"
+#'
+#' @return A \code{SpatialExperiment} object with one sample per group specified
+#' in \code{sample_info} using transformed pixel and array coordinates (including
+#' in the \code{spatialCoords}).
+#'
+#' @import SpatialExperiment
+#' @importFrom readr read_csv
+#' @importFrom dplyr mutate as_tibble
+#' @export
+#' @author Nicholas J. Eagles
+#' 
+#' @examples
+#' #   For internal testing
+#' \dontrun{
+#'     sample_info = readr::read_csv('dev/test_data/sample_info.csv')
+#'     coords_dir = 'dev/test_data'
+#'     metric_name = 'sum_umi'
+#'     spe = build_spe(sample_info, coords_dir, metric_name)
+#' }
+
+build_spe = function(sample_info, coords_dir, metric_name, count_type = "sparse") {
+    message("Building SpatialExperiment using capture area as sample ID")
+    spe <- read10xVisium(
+        samples = dirname(sample_info$spaceranger_dir),
+        sample_id = sample_info$capture_area,
+        type = count_type,
+        data = "raw",
+        images = "lowres",
+        load = FALSE
+    )
+
+    message("Overwriting imgData(spe) with merged images (one per group)")
+    all_groups = unique(sample_info$group)
+
+    img_data <- readImgData(
+        path = file.path(coords_dir, all_groups),
+        sample_id = all_groups,
+        imageSources = file.path(
+            coords_dir, all_groups, "tissue_lowres_image.png"
+        ),
+        scaleFactors = file.path(
+            coords_dir, all_groups, "scalefactors_json.json"
+        ),
+        load = TRUE
+    )
+
+    coldata_fixed = colData(spe) |>
+        dplyr::as_tibble() |>
+        dplyr::mutate(
+            capture_area = factor(sample_id),
+            group = factor(
+                sample_info$group[
+                    match(capture_area, sample_info$capture_area)
+                ]
+            ),
+            sample_id = group,
+            barcode = colnames(spe),
+            key = paste(barcode, capture_area, sep = "_")
+        )
+
+    spe <- SpatialExperiment(
+        assays = assays(spe),
+        rowData = rowData(spe),
+        colData = coldata_fixed,
+        spatialCoords = spatialCoords(spe),
+        imgData = img_data
+    )
+
+    spe = add_array_coords(spe, sample_info, coords_dir, overwrite = TRUE)
+    spe = add_overlap_info(spe, metric_name)
+
+    return(spe)
+}