alabaster.bumpy 1.8.0
The BumpyMatrix class provides a representation of complex ragged data structures - see the BumpyMatrix package for more information.
This is used to coerce immune repertoire, spatial transcriptomics and drug response data into a familiar 2D array for easy manipulation.
The alabaster.bumpy package allows users to save a BumpyMatrix to file within the alabaster framework.
BumpyMatrixLet’s make a BumpyMatrix to demonstrate:
library(BumpyMatrix)
library(S4Vectors)
df <- DataFrame(x=runif(100), y=runif(100))
f <- factor(sample(letters[1:20], nrow(df), replace=TRUE), letters[1:20])
mat <- BumpyMatrix(split(df, f), c(5, 4))Saving it to file involves calling saveObject:
library(alabaster.bumpy)
tmp <- tempfile()
saveObject(mat, tmp)
list.files(tmp, recursive=TRUE)## [1] "OBJECT" "_environment.json"
## [3] "concatenated/OBJECT" "concatenated/basic_columns.h5"
## [5] "partitions.h5"BumpyMatrixThe loading procedure is even simpler as the metadata of the saved BumpyMatrix remembers how it was saved.
We can just use alabaster.base::readObject() or related functions, and the R interface will automatically do the rest.
readObject(tmp)## 5 x 4 BumpyDataFrameMatrix
## rownames: NULL
## colnames: NULL
## preview [1,1]:
## DataFrame with 3 rows and 2 columns
## x y
## <numeric> <numeric>
## 1 0.647901 0.312269
## 2 0.900158 0.517649
## 3 0.073839 0.290322sessionInfo()## R version 4.5.0 RC (2025-04-04 r88126)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.2 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.21-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.12.0 LAPACK version 3.12.0
##
## locale:
## [1] LC_CTYPE=en_US.UTF-8 LC_NUMERIC=C
## [3] LC_TIME=en_GB 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: America/New_York
## tzcode source: system (glibc)
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] alabaster.bumpy_1.8.0 alabaster.base_1.8.0 S4Vectors_0.46.0
## [4] BiocGenerics_0.54.0 generics_0.1.3 BumpyMatrix_1.16.0
## [7] BiocStyle_2.36.0
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.4 knitr_1.50 rlang_1.1.6
## [4] xfun_0.52 jsonlite_2.0.0 htmltools_0.5.8.1
## [7] sass_0.4.10 rmarkdown_2.29 grid_4.5.0
## [10] evaluate_1.0.3 jquerylib_0.1.4 fastmap_1.2.0
## [13] Rhdf5lib_1.30.0 alabaster.schemas_1.8.0 yaml_2.3.10
## [16] IRanges_2.42.0 lifecycle_1.0.4 bookdown_0.43
## [19] BiocManager_1.30.25 compiler_4.5.0 Rcpp_1.0.14
## [22] rhdf5filters_1.20.0 rhdf5_2.52.0 lattice_0.22-7
## [25] digest_0.6.37 R6_2.6.1 bslib_0.9.0
## [28] Matrix_1.7-3 tools_4.5.0 cachem_1.1.0