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
:
## [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.
## 5 x 4 BumpyDataFrameMatrix
## rownames: NULL
## colnames: NULL
## preview [1,1]:
## DataFrame with 6 rows and 2 columns
## x y
## <numeric> <numeric>
## 1 0.695630 0.458503
## 2 0.827427 0.268151
## 3 0.791114 0.357757
## 4 0.517961 0.509075
## 5 0.657381 0.897133
## 6 0.790857 0.733441
## R version 4.4.1 (2024-06-14)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04 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] alabaster.bumpy_1.5.0 alabaster.base_1.5.6 S4Vectors_0.43.2
## [4] BiocGenerics_0.51.0 BumpyMatrix_1.13.0 BiocStyle_2.33.1
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.3 knitr_1.48 rlang_1.1.4
## [4] xfun_0.47 jsonlite_1.8.8 buildtools_1.0.0
## [7] htmltools_0.5.8.1 maketools_1.3.0 sys_3.4.2
## [10] sass_0.4.9 rmarkdown_2.28 grid_4.4.1
## [13] evaluate_0.24.0 jquerylib_0.1.4 fastmap_1.2.0
## [16] Rhdf5lib_1.27.0 alabaster.schemas_1.5.0 yaml_2.3.10
## [19] IRanges_2.39.2 lifecycle_1.0.4 BiocManager_1.30.25
## [22] compiler_4.4.1 Rcpp_1.0.13 rhdf5filters_1.17.0
## [25] rhdf5_2.49.0 lattice_0.22-6 digest_0.6.37
## [28] R6_2.5.1 bslib_0.8.0 Matrix_1.7-0
## [31] tools_4.4.1 cachem_1.1.0