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 7 rows and 2 columns
## x y
## <numeric> <numeric>
## 1 0.368499090 0.7654708
## 2 0.460964945 0.0926092
## 3 0.000115619 0.2594357
## 4 0.836377023 0.9220393
## 5 0.230115704 0.3862117
## 6 0.244107045 0.6793082
## 7 0.160395808 0.5338643
sessionInfo()
## R version 4.4.0 RC (2024-04-16 r86468)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 22.04.4 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.20-bioc/R/lib/libRblas.so
## LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.10.0
##
## 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_1.5.0 alabaster.base_1.5.0 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