alabaster.bumpy 1.5.0
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.
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" "concatenated/OBJECT"
## [3] "concatenated/basic_columns.h5" "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 8 rows and 2 columns
## x y
## <numeric> <numeric>
## 1 0.6075783 0.149085
## 2 0.9269073 0.281184
## 3 0.0416181 0.145733
## 4 0.2151126 0.871177
## 5 0.8747261 0.578105
## 6 0.3549096 0.210763
## 7 0.6351554 0.609028
## 8 0.6989676 0.363033
sessionInfo()
## R version 4.4.0 Patched (2024-04-24 r86482)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.6.6
##
## Matrix products: default
## BLAS: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRblas.0.dylib
## LAPACK: /Library/Frameworks/R.framework/Versions/4.4-arm64/Resources/lib/libRlapack.dylib; LAPACK version 3.12.0
##
## 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_1.5.0 alabaster.base_1.5.1 S4Vectors_0.43.0
## [4] BiocGenerics_0.51.0 BumpyMatrix_1.13.0 BiocStyle_2.33.0
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.2 knitr_1.46 rlang_1.1.3
## [4] xfun_0.43 jsonlite_1.8.8 htmltools_0.5.8.1
## [7] sass_0.4.9 rmarkdown_2.26 grid_4.4.0
## [10] evaluate_0.23 jquerylib_0.1.4 fastmap_1.1.1
## [13] Rhdf5lib_1.27.0 alabaster.schemas_1.5.0 yaml_2.3.8
## [16] IRanges_2.39.0 lifecycle_1.0.4 bookdown_0.39
## [19] BiocManager_1.30.22 compiler_4.4.0 Rcpp_1.0.12
## [22] rhdf5filters_1.17.0 rhdf5_2.49.0 lattice_0.22-6
## [25] digest_0.6.35 R6_2.5.1 bslib_0.7.0
## [28] Matrix_1.7-0 tools_4.4.0 cachem_1.0.8