Merge branch 'main' into devel

pachterlab · Jan 2, 2025 · 761c859 · 761c859
2 parents 0803d83 + 21d4666
commit 761c859
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Showing 2 changed files with 11 additions and 8 deletions.
diff --git a/R/aggregate.R b/R/aggregate.R
@@ -216,17 +216,20 @@ aggregateTxTech <- function(data_dir, df = NULL, by = NULL,
 
     # Probably faster than directly calling st_intersection, since I don't need
     # the actual geometries of the intersections, maybe not
-    tx_coords <- st_coordinates(rg) # Might write another function similar to formatTxTech to skip this
-    tx_point <- df2sf(tx_coords, spatialCoordsNames = c("X", "Y", "Z"))
+    tx_coords <- st_coordinates(rg)
+    if (ncol(tx_coords) > 3L) scn <- c("X", "Y", "Z") else scn <- c("X", "Y")
+    tx_point <- df2sf(tx_coords, spatialCoordsNames = scn)
     tx_ind <- as.data.table(st_drop_geometry(tx_point))
     tx_info <- txSpots(x) |> st_drop_geometry()
     tx_info$L1 <- seq_along(tx_info$gene) # it has to be "gene" if it's from formatTxSpots
     tx_point <- merge(tx_point, tx_info, by = "L1") # takes a while
     tx_point <- st_as_sf(tx_point) |> st_join(grid_sf) # takes a few minutes
     tx_counts <- tx_point |> st_drop_geometry() |> as.data.table()
     tx_counts <- tx_counts[, .N, by = .(gene, L1, grid_id)]
-
-    new_mat <- sparseMatrix(i = tx_counts$L1, j = tx_counts$grid_id, x = tx_counts$N)
+    # When some spots are outside the grids
+    tx_counts <- tx_counts[!is.na(grid_id),]
+    new_mat <- sparseMatrix(i = tx_counts$L1, j = tx_counts$grid_id, x = tx_counts$N,
+                            dims = c(nrow(x), max(tx_counts$grid_id)))
     cgs <- list(bins = grid_sf)
     names(cgs) <- new_geometry_name
     out <- SpatialFeatureExperiment(assays = list(counts = new_mat),

diff --git a/R/read.R b/R/read.R
@@ -986,10 +986,10 @@ readCosMX <- function(data_dir,
                       z_option = c("3d", "split")) {
     check_installed("sfarrow")
     data_dir <- normalizePath(data_dir, mustWork = TRUE)
-    fns <- list.files(data_dir, pattern = "\\.csv$", full.names = TRUE)
-    fn_metadata <- grep("metadata", fns, value = TRUE)
-    fn_mat <- grep("exprMat", fns, value = TRUE)
-    fn_polys <- grep("polygons", fns, value = TRUE)
+    fns <- list.files(data_dir, pattern = "\\.csv.*$", full.names = TRUE)
+    fn_metadata <- grep("metadata", fns, value = TRUE)[1]
+    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