alabaster.bumpy 1.9.1
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.
BumpyMatrix
Let’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"
BumpyMatrix
The 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 6 rows and 2 columns
## x y
## <numeric> <numeric>
## 1 0.255011 0.178042
## 2 0.228359 0.332369
## 3 0.770520 0.981256
## 4 0.815193 0.535563
## 5 0.782200 0.979165
## 6 0.273596 0.827745
sessionInfo()
## R version 4.5.0 Patched (2025-04-21 r88169)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.1
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.1
##
## locale:
## [1] C/en_US.UTF-8/en_US.UTF-8/C/en_US.UTF-8/en_US.UTF-8
##
## time zone: America/New_York
## tzcode source: internal
##
## attached base packages:
## [1] stats4 stats graphics grDevices utils datasets methods
## [8] base
##
## other attached packages:
## [1] alabaster.bumpy_1.9.1 alabaster.base_1.9.0 S4Vectors_0.47.0
## [4] BiocGenerics_0.55.0 generics_0.1.4 BumpyMatrix_1.17.0
## [7] BiocStyle_2.37.0
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.5 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_1.31.0 alabaster.schemas_1.9.0 yaml_2.3.10
## [16] IRanges_2.43.0 lifecycle_1.0.4 bookdown_0.43
## [19] BiocManager_1.30.25 compiler_4.5.0 Rcpp_1.0.14
## [22] rhdf5filters_1.21.0 rhdf5_2.53.0 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