The alabaster.matrix package implements methods to save matrix-like objects to file artifacts and load them back into R. Check out the alabaster.base for more details on the motivation and the alabaster framework.
Given an array-like object, we can use saveObject() to
save it inside a staging directory:
library(Matrix)
y <- rsparsematrix(1000, 100, density=0.05)
library(alabaster.matrix)
tmp <- tempfile()
saveObject(y, tmp)
list.files(tmp, recursive=TRUE)## [1] "OBJECT" "matrix.h5"We then load it back into our R session with
loadObject(). This creates a HDF5-backed S4 array that can
be easily coerced into the desired format, e.g., a
dgCMatrix.
## [1] "ReloadedMatrix"
## attr(,"package")
## [1] "alabaster.matrix"This process is supported for all base arrays, Matrix objects and DelayedArray objects.
For DelayedArrays, we may instead choose to save the
delayed operations themselves to file. This creates a HDF5 file
following the chihaya
format, containing the delayed operations rather than the results of
their evaluation.
library(DelayedArray)
y <- DelayedArray(rsparsematrix(1000, 100, 0.05))
y <- log1p(abs(y) / 1:100) # adding some delayed ops.
tmp <- tempfile()
saveObject(y, tmp, DelayedArray.preserve.ops=TRUE)
# Inspecting the HDF5 file reveals many delayed operations:
rhdf5::h5ls(file.path(tmp, "array.h5"))## group name otype dclass dim
## 0 / delayed_array H5I_GROUP
## 1 /delayed_array method H5I_DATASET STRING ( 0 )
## 2 /delayed_array seed H5I_GROUP
## 3 /delayed_array/seed along H5I_DATASET INTEGER ( 0 )
## 4 /delayed_array/seed method H5I_DATASET STRING ( 0 )
## 5 /delayed_array/seed seed H5I_GROUP
## 6 /delayed_array/seed/seed method H5I_DATASET STRING ( 0 )
## 7 /delayed_array/seed/seed seed H5I_GROUP
## 8 /delayed_array/seed/seed/seed by_column H5I_DATASET INTEGER ( 0 )
## 9 /delayed_array/seed/seed/seed data H5I_DATASET FLOAT 5000
## 10 /delayed_array/seed/seed/seed dimnames H5I_GROUP
## 11 /delayed_array/seed/seed/seed indices H5I_DATASET INTEGER 5000
## 12 /delayed_array/seed/seed/seed indptr H5I_DATASET INTEGER 101
## 13 /delayed_array/seed/seed/seed shape H5I_DATASET INTEGER 2
## 14 /delayed_array/seed side H5I_DATASET STRING ( 0 )
## 15 /delayed_array/seed value H5I_DATASET INTEGER 1000## <1000 x 100> sparse ReloadedMatrix object of type "double":
## [,1] [,2] [,3] ... [,99] [,100]
## [1,] 0 0 0 . 0.0000000 0.0000000
## [2,] 0 0 0 . 0.0000000 0.0000000
## [3,] 0 0 0 . 0.2725684 0.0000000
## [4,] 0 0 0 . 0.0000000 0.0000000
## [5,] 0 0 0 . 0.0000000 0.0000000
## ... . . . . . .
## [996,] 0 0 0 . 0.000000000 0.000000000
## [997,] 0 0 0 . 0.000000000 0.000000000
## [998,] 0 0 0 . 0.006002358 0.000000000
## [999,] 0 0 0 . 0.000000000 0.000000000
## [1000,] 0 0 0 . 0.000000000 0.008265744This allows users to avoid evaluation of the operations when saving objects, which may improve efficiency, e.g., by avoiding loss of sparsity or casting to a larger type.
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 LTS
##
## Matrix products: default
## BLAS: /usr/lib/x86_64-linux-gnu/openblas-pthread/libblas.so.3
## LAPACK: /usr/lib/x86_64-linux-gnu/openblas-pthread/libopenblasp-r0.3.26.so; LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_US.UTF-8 LC_COLLATE=C
## [5] LC_MONETARY=en_US.UTF-8 LC_MESSAGES=en_US.UTF-8
## [7] LC_PAPER=en_US.UTF-8 LC_NAME=C
## [9] LC_ADDRESS=C LC_TELEPHONE=C
## [11] LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C
##
## time zone: Etc/UTC
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] DelayedArray_0.33.3 SparseArray_1.7.2 S4Arrays_1.7.1
## [4] abind_1.4-8 IRanges_2.41.2 S4Vectors_0.45.2
## [7] MatrixGenerics_1.19.0 matrixStats_1.4.1 BiocGenerics_0.53.3
## [10] generics_0.1.3 alabaster.matrix_1.7.4 alabaster.base_1.7.2
## [13] Matrix_1.7-1 BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] jsonlite_1.8.9 compiler_4.4.2 BiocManager_1.30.25
## [4] crayon_1.5.3 Rcpp_1.0.13-1 rhdf5filters_1.19.0
## [7] jquerylib_0.1.4 yaml_2.3.10 fastmap_1.2.0
## [10] lattice_0.22-6 XVector_0.47.0 R6_2.5.1
## [13] knitr_1.49 maketools_1.3.1 bslib_0.8.0
## [16] rlang_1.1.4 HDF5Array_1.35.2 cachem_1.1.0
## [19] xfun_0.49 sass_0.4.9 sys_3.4.3
## [22] cli_3.6.3 Rhdf5lib_1.29.0 zlibbioc_1.52.0
## [25] digest_0.6.37 grid_4.4.2 alabaster.schemas_1.7.0
## [28] rhdf5_2.51.0 lifecycle_1.0.4 evaluate_1.0.1
## [31] buildtools_1.0.0 rmarkdown_2.29 tools_4.4.2
## [34] htmltools_0.5.8.1