move to v0.2.6 (#280)

move to v0.2.6

Author: Artur-man

.github/workflows/check.yml

@@ -21,10 +21,11 @@ jobs:
       fail-fast: false
       matrix:
         config:
+          - {os: macos-latest,   r: 'devel'}
           - {os: macos-latest,   r: 'release'}
-          - {os: windows-latest, r: 'release', rtools-version: '44'}
-          - {os: ubuntu-latest,   r: 'release'}
-          - {os: ubuntu-24.04,   r: 'release'}
+          - {os: windows-latest, r: 'devel', rtools-version: '45'}
+          - {os: ubuntu-latest,   r: 'devel'}
+          - {os: ubuntu-24.04,   r: 'devel'}
 
     steps:
 

DESCRIPTION

@@ -1,8 +1,8 @@
 Package: VoltRon
 Type: Package
 Title: VoltRon for Spatial Omics Data Integration and Analysis
-Version: 0.2.5
-Depends: R (>= 4.4.0)
+Version: 0.2.6
+Depends: R (>= 4.6.0)
 Author@R: 
 	person("Artür", "Manukyan", 
 		     role=c("aut", "cre"),
@@ -69,6 +69,7 @@ Suggests:
     BiocParallel,
     rhdf5,
     Rarr,
+    ZarrArray,
     basilisk,
     reticulate,
     RBioFormats,
@@ -104,13 +105,12 @@ Suggests:
     anndata,
     SimpleITK
 Remotes:
-	stla/RCDT,
+	  stla/RCDT,
     BIMSBbioinfo/VoltRonStore,
     bnprks/BPCells/r@v0.3.0,
     BIMSBbioinfo/VoltRon,
     BIMSBbioinfo/HDF5DataFrame,
-    BIMSBbioinfo/ZarrDataFrame,
-    Artur-man/ImageArray
+    BIMSBbioinfo/ZarrDataFrame
 Config/testthat/edition: 3
 LazyData: true
 LazyDataCompression: gzip

Dockerfile

@@ -14,7 +14,7 @@ RUN R -e "install.packages(c('shiny', 'devtools', 'BiocManager'), repos='http://
 
 # Install VoltRon dependencies
 RUN R -e "install.packages(c('grDevices', 'data.table', 'RcppAnnoy', 'RANN', 'Matrix', 'dplyr', 'ggplot2', 'ggrepel', 'igraph', 'rjson', 'magick', 'ids', 'sp', 'reshape2', 'rlang', 'ggpubr', 'shinyjs'), repos='http://cran.rstudio.com/')"
-RUN R -e "install.packages(c('stringr', 'uwot'), repos='http://cran.rstudio.com/')"
+RUN R -e "install.packages(c('remotes', 'stringr', 'uwot'), repos='http://cran.rstudio.com/')"
 RUN R -e "BiocManager::install(c('EBImage', 'S4Arrays', 'BiocSingular'))"
 
 # set up java

R/image.R

@@ -177,8 +177,8 @@ subsetvrImage <- function(x, subset, spatialpoints = NULL, image = NULL) {
         img_data <- ImageArray::crop(
           img_data,
           ind = list(
-            crop_info_int[3]:(crop_info_int[3] + crop_info_int[1]),
-            crop_info_int[4]:(crop_info_int[4] + crop_info_int[2])
+            x = crop_info_int[3]:(crop_info_int[3] + crop_info_int[1]),
+            y = crop_info_int[4]:(crop_info_int[4] + crop_info_int[2])
           )
         )
         object@image[[img]] <- img_data

R/ondisk.R

@@ -747,9 +747,9 @@ writeHDF5ArrayInImage <- function(
           img <-
             ImageArray::writeImageArray(
               img,
-              output = gsub(".h5$", "", h5_path),
+              output = h5_path,
               name = paste0(name, "/spat_", spat, "/", ch),
-              format = "HDF5ImageArray",
+              format = "hdf5",
               replace = FALSE,
               chunkdim = chunkdim,
               level = level,
@@ -784,16 +784,18 @@ writeHDF5ArrayInImage <- function(
          remotes::install_github('bnprks/BPCells/r')"
       )
     }
-    # if (!inherits(object, "dgCMatrix")) {
-    if (!inherits(object, "Matrix")) {
+    if (!inherits(object, "CsparseMatrix")) {
       object <- as(object, "dgCMatrix")
     }
-    object <- BPCells::write_matrix_hdf5(
-      object,
-      path = h5_path,
-      group = name,
-      overwrite = TRUE
-    )
+    # save only when the data is non zero length
+    if(nrow(object) > 0){
+      object <- BPCells::write_matrix_hdf5(
+        object,
+        path = h5_path,
+        group = name,
+        overwrite = TRUE
+      ) 
+    }
   } else if (feature.vs.obs.engine == "DelayedArray") {
     if (!requireNamespace('HDF5Array')) {
       stop(
@@ -1001,13 +1003,13 @@ writeZarrArrayInMetadata <- function(
           }
           cur_column <- as.array(cur_column)
           meta.data_list[["id"]] <-
-            Rarr::writeZarrArray(
+            ZarrArray::writeZarrArray(
               cur_column,
-              zarr_array_path = file.path(
+              zarr_path = file.path(
                 zarr_path,
                 paste0(name, "/", sn, "/id")
               ),
-              chunk_dim = min(length(cur_column), 2000),
+              chunkdim = min(length(cur_column), 2000),
               nchar = nchar
             )
         }
@@ -1028,13 +1030,13 @@ writeZarrArrayInMetadata <- function(
           }
           cur_column <- as.array(cur_column)
           meta.data_list[[colnames(meta.data)[i]]] <-
-            Rarr::writeZarrArray(
+            ZarrArray::writeZarrArray(
               cur_column,
-              zarr_array_path = file.path(
+              zarr_path = file.path(
                 zarr_path,
                 paste0(name, "/", sn, "/", colnames(meta.data)[i])
               ),
-              chunk_dim = min(length(cur_column), 2000),
+              chunkdim = min(length(cur_column), 2000),
               nchar = nchar
             )
         }
@@ -1092,10 +1094,10 @@ writeZarrArrayInVrData <- function(
           if (!is.array(a)) {
             a <- as.array(a)
           }
-          a <- Rarr::writeZarrArray(
+          a <- ZarrArray::writeZarrArray(
             a,
-            zarr_array_path = file.path(zarr_path, paste0(name, "/", feat)),
-            chunk_dim = chunkdim
+            zarr_path = file.path(zarr_path, paste0(name, "/", feat)),
+            chunkdim = chunkdim
           )
         } else {
           a <- DelayedArray::DelayedArray(a)
@@ -1121,13 +1123,13 @@ writeZarrArrayInVrData <- function(
           if (!is.array(a)) {
             a <- as.array(a)
           }
-          a <- Rarr::writeZarrArray(
+          a <- ZarrArray::writeZarrArray(
             a,
-            zarr_array_path = file.path(
+            zarr_path = file.path(
               zarr_path,
               paste0(name, "/", feat, "_norm")
             ),
-            chunk_dim = chunkdim
+            chunkdim = chunkdim
           )
         } else {
           a <- DelayedArray::DelayedArray(a)
@@ -1157,10 +1159,10 @@ writeZarrArrayInVrData <- function(
         if (!is.array(a)) {
           a <- as.array(a)
         }
-        a <- Rarr::writeZarrArray(
+        a <- ZarrArray::writeZarrArray(
           a,
-          zarr_array_path = file.path(zarr_path, paste0(name, "/rawdata")),
-          chunk_dim = chunkdim
+          zarr_path = file.path(zarr_path, paste0(name, "/rawdata")),
+          chunkdim = chunkdim
         )
       } else {
         a <- DelayedArray::DelayedArray(a)
@@ -1186,10 +1188,10 @@ writeZarrArrayInVrData <- function(
         if (!is.array(a)) {
           a <- as.array(a)
         }
-        a <- Rarr::writeZarrArray(
+        a <- ZarrArray::writeZarrArray(
           a,
-          zarr_array_path = file.path(zarr_path, paste0(name, "/normdata")),
-          chunk_dim = chunkdim
+          zarr_path = file.path(zarr_path, paste0(name, "/normdata")),
+          chunkdim = chunkdim
         )
       } else {
         a <- DelayedArray::DelayedArray(a)
@@ -1248,13 +1250,13 @@ writeZarrArrayInImage <- function(
       if (is.null(chunkdim)) {
         chunkdim <- vapply(dim(coords), function(x) min(x, 1000), numeric(1))
       }
-      coords <- Rarr::writeZarrArray(
+      coords <- ZarrArray::writeZarrArray(
         coords,
-        zarr_array_path = file.path(
+        zarr_path = file.path(
           zarr_path,
           paste0(name, "/spat_", spat, "/coords")
         ),
-        chunk_dim = chunkdim
+        chunkdim = chunkdim
       )
 
       # Rarr::ZarrArray doesnt have rownames
@@ -1285,9 +1287,9 @@ writeZarrArrayInImage <- function(
           }
           img <- ImageArray::writeImageArray(
             img,
-            output = gsub(".zarr$", "", zarr_path),
+            output = zarr_path,
             name = paste0(name, "/spat_", spat, "/", ch),
-            format = "ZarrImageArray",
+            format = "zarr",
             replace = FALSE,
             chunkdim = chunkdim,
             level = level,

R/registration.R

@@ -2250,7 +2250,7 @@ plotImage <- function(image, max.pixel.size = NULL) {
     }
     imgggplot <- magick::image_ggplot(image)
   } else if (inherits(image, "ImageArray")) {
-    img_raster <- ImageArray::as.raster(image, max.pixel.size = max.pixel.size)
+    img_raster <- as.raster(image, max.pixel.size = max.pixel.size)
     info <- list(width = dim(img_raster)[2], height = dim(img_raster)[1])
     imgggplot <- ggplot2::ggplot(
       data.frame(x = 0, y = 0),
@@ -2398,8 +2398,8 @@ cropImage <- function(image, geometry) {
     image <- ImageArray::crop(
       image,
       ind = list(
-        crop_info_int[3]:(crop_info_int[3] + crop_info_int[1]),
-        crop_info_int[4]:(crop_info_int[4] + crop_info_int[2])
+        x = crop_info_int[3]:(crop_info_int[3] + crop_info_int[1]),
+        y = crop_info_int[4]:(crop_info_int[4] + crop_info_int[2])
       )
     )
   }

R/visualization.R

@@ -2421,7 +2421,7 @@ vrSpatialPlotImage <- function(
 
       # TODO: is this necessary ?
       if (inherits(image, "ImageArray")) {
-        image <- ImageArray::as.raster(image)
+        image <- as.raster(image)
       }
 
       # annotation raster

tests/testthat/test-ondisk.R

@@ -6,6 +6,7 @@ skip_if_not_installed("HDF5DataFrame")
 skip_if_not_installed("ZarrDataFrame")
 skip_if_not_installed("ImageArray")
 skip_if_not_installed("BPCells")
+skip_if_not_installed("DelayedMatrixStats")
 
 # create dir
 dir.create(td <- tempfile())