Updated load10XCoords to be able to read tissue positions from Visium…

…HD which are stored in .parquet files. Added the nanoparquet function to depends in DESCRIPTION as well as updated package version. Added spatialDir to an argument in load10XCoords since VisiumHD typically has a separate folders for each of the resolutions each with their own spatial folder.

DESCRIPTION

@@ -1,7 +1,7 @@
 Type: Package
 Package: SpaceMarkers
 Title: Spatial Interaction Markers
-Version: 1.1.6
+Version: 1.1.7
 Authors@R: c(
     person(given = "Atul", family = "Deshpande", email = "[email protected]", role = c("aut", "cre"), comment = c(ORCID="0000-0001-5144-6924")),
     person(given = "Ludmila", family = "Danilova", email = "[email protected]", role = "ctb"),
@@ -27,6 +27,7 @@ Imports:
     ape,
     hdf5r,
     jsonlite,
+    nanoparquet,
     Matrix,
     qvalue,
     stats,

R/preprocessing.R

@@ -96,7 +96,8 @@ load10XExpr<- function(visiumDir=NULL,
 #' unlink("Visium_Human_Breast_Cancer_spatial.tar.gz")
 #' 
 
-load10XCoords <- function(visiumDir, resolution = "lowres", version = NULL){
+load10XCoords <- function(visiumDir, resolution = "lowres", version = NULL,
+                          spatialDir = "spatial"){
     #determine spacerager version
     if(is.null(version)){
         message("Version not provided. Trying to infer.")
@@ -116,15 +117,22 @@ load10XCoords <- function(visiumDir, resolution = "lowres", version = NULL){
         has_header <- TRUE
         tissue_pos_name <- "tissue_positions.csv"
     }
-    spatial_dir <- paste0(visiumDir,'/spatial')
-    scale_json <- dir(spatial_dir,
-                        pattern = "scalefactors_json.json",full.names = TRUE)
-    scale_values <- jsonlite::read_json(scale_json)
-    scale_factor <- scale_values[grepl(resolution, names(scale_values))][[1]]
+  spatial_dir <- file.path(visiumDir,spatialDir)
+  scale_json <- dir(spatial_dir,
+                    pattern = "scalefactors_json.json",full.names = TRUE)
+  scale_values <- jsonlite::read_json(scale_json)
+  scale_factor <- scale_values[grepl(resolution, names(scale_values))][[1]]
+  # account for visiumHD
+  if (version == "1.0" | version == "2.0"){
     coord_file <- dir(spatial_dir,
-                        pattern = tissue_pos_name, full.names = TRUE)
-
+                      pattern = tissue_pos_name, full.names = TRUE)
     coord_values <- read.csv(coord_file, header = has_header)
+  } else if (version == "3.0") {
+    tissue_pos_name <- "tissue_positions.parquet"
+    coord_file <- dir(spatial_dir,
+                      pattern = tissue_pos_name, full.names = TRUE)
+    coord_values <- nanoparquet::read_parquet(coord_file)
+  }
     coord_values <- coord_values[,c(1,5,6)]
     coord_values[,2:3] <- coord_values[,2:3]*scale_factor
     names(coord_values) <- c("barcode","y","x")