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minor changes to readCoSMX #79

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minor changes to readCoSMX #79

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29 changes: 15 additions & 14 deletions R/read.R
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Original file line number Diff line number Diff line change
Expand Up @@ -995,21 +995,8 @@ readCosMX <- function(data_dir,
fn_mat <- grep("exprMat", fns, value = TRUE)[1]
fn_polys <- grep("polygons", fns, value = TRUE)[1]

meta <- fread(fn_metadata)
mat <- fread(fn_mat) # TODO: write to h5 or mtx. Consult alabaster.sce


meta$cell_ID <- paste(meta$cell_ID, meta$fov, sep = "_")
mat$cell_ID <- paste(mat$cell_ID, mat$fov, sep = "_")

mat <- mat[match(meta$cell_ID, mat$cell_ID),]
cell_ids <- mat$cell_ID
mat <- mat[,3:ncol(mat)] |>
as.matrix() |>
as("CsparseMatrix") |> Matrix::t()
colnames(mat) <- cell_ids

poly_sf_fn <- file.path(data_dir, "cell_boundaries_sf.parquet")

if (file.exists(poly_sf_fn)) {
message(">>> File cell_boundaries_sf.parquet found")
polys <- sfarrow::st_read_parquet(poly_sf_fn)
Expand All @@ -1027,6 +1014,20 @@ readCosMX <- function(data_dir,
suppressWarnings(sfarrow::st_write_parquet(polys, poly_sf_fn))
}

meta <- fread(fn_metadata) |>
dplyr::mutate(cell_ID = paste(cell_ID, fov, sep = "_")) |>
dplyr::filter(cell_ID %in% polys$cellID)
mat <- fread(fn_mat) |> # TODO: write to h5 or mtx. Consult alabaster.sce
dplyr::mutate(cell_ID = paste(cell_ID, fov, sep = "_")) |>
dplyr::filter(cell_ID %in% polys$cellID)

mat <- mat[match(meta$cell_ID, mat$cell_ID),]
cell_ids <- mat$cell_ID
mat <- mat[,3:ncol(mat)] |>
as.matrix() |>
as("CsparseMatrix") |> Matrix::t()
colnames(mat) <- cell_ids

sfe <- SpatialFeatureExperiment(list(counts = mat), colData = meta,
sample_id = sample_id,
spatialCoordsNames = c("CenterX_global_px", "CenterY_global_px"),
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