Merge branch 'devel' of https://github.com/pachterlab/SpatialFeatureE…

…xperiment into devel

R/read.R

@@ -460,7 +460,6 @@ read10xVisiumSFE <- function(samples = "",
 
 # sanity on geometries to remove any self-intersection
 #' @importFrom sf st_buffer st_is_valid
-# TODO: this needs to be optimized, takes too long for real data ----
 .check_st_valid <- function(sf_df = NULL) {
     # sf_df is a single sf data frame, not a list of sf data frames
     invalid_inds <- which(!st_is_valid(sf_df))
@@ -475,7 +474,9 @@ read10xVisiumSFE <- function(samples = "",
         }
         old_type <- st_geometry_type(sf_df, by_geometry = FALSE)
         if (new_type != old_type && new_type != "GEOMETRY") {
-            sf_df <- st_cast(sf_df, as.character(new_type))
+            sf_df <- sfheaders::sf_cast(sf_df, as.character(new_type))
+            # sf::st_cast can take too long
+            #sf_df <- st_cast(sf_df, as.character(new_type))
         }
         st_geometry(sf_df)[invalid_inds] <- geoms_new
     }
@@ -726,7 +727,7 @@ readVizgen <- function(data_dir,
     meta_fn <- .check_vizgen_fns(data_dir, "cell_metadata")
     metadata <- fread(meta_fn, colClasses = list(character = 1))
     if (any(names(metadata) == "transcript_count") && filter_counts) {
-        message(">>> ..filtering `cell_metadata` - keep cells with `transcript_count` > 0")
+        message(">>> filtering `cell_metadata` - keep cells with `transcript_count` > 0")
         metadata <- metadata[metadata$transcript_count > 0,]
     }
 
@@ -988,8 +989,8 @@ readCosMX <- function(data_dir,
 #' @note Sometimes when reading images, you will see this error the first time:
 #' 'java.lang.NullPointerException: Cannot invoke
 #' "loci.formats.DimensionSwapper.setMetadataFiltered(boolean)" because
-#' "RBioFormats.reader" is null'. Rerun the code and it should work the second
-#' time.
+#' "RBioFormats.reader" is null'. See this issue https://github.com/aoles/RBioFormats/issues/42 
+#' Rerun the code and it should work the second time.
 #' @export
 #' @concept Read data into SFE
 #' @importFrom sf st_area st_geometry<- st_as_sf
@@ -1236,8 +1237,8 @@ readXenium <- function(data_dir,
     # Filtering count matrix, metadata and segmentations ----
     # filtering metadata and count matrix
     if (any(names(metadata) == "transcript_counts") && filter_counts) {
-        message(">>> ..filtering cell metadata - keep cells with `transcript_counts` > 0")
-        metadata <- metadata[metadata$transcript_count > 0,]
+        message(">>> filtering cell metadata - keep cells with `transcript_counts` > 0")
+        metadata <- metadata[metadata$transcript_counts > 0,]
         sce <- sce[,match(metadata$cell_id, colnames(sce)) |> na.omit()]
     } else {
         # if metadata isn't already filtered