alabaster.bumpy 1.4.0
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 9 rows and 2 columns
## x y
## <numeric> <numeric>
## 1 0.81536516 0.1315107
## 2 0.21668294 0.7075564
## 3 0.76777935 0.3963126
## 4 0.92621753 0.4460723
## 5 0.24820521 0.0117569
## 6 0.73103439 0.3524498
## 7 0.47054186 0.0732900
## 8 0.88264719 0.4863902
## 9 0.00845114 0.1489473
sessionInfo()
## R version 4.4.0 beta (2024-04-15 r86425 ucrt)
## Platform: x86_64-w64-mingw32/x64
## Running under: Windows Server 2022 x64 (build 20348)
##
## Matrix products: default
##
##
## locale:
## [1] LC_COLLATE=C
## [2] LC_CTYPE=English_United States.utf8
## [3] LC_MONETARY=English_United States.utf8
## [4] LC_NUMERIC=C
## [5] LC_TIME=English_United States.utf8
##
## 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_1.4.0 alabaster.base_1.4.0 S4Vectors_0.42.0
## [4] BiocGenerics_0.50.0 BumpyMatrix_1.12.0 BiocStyle_2.32.0
##
## 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_1.26.0 alabaster.schemas_1.4.0 yaml_2.3.8
## [16] IRanges_2.38.0 lifecycle_1.0.4 bookdown_0.39
## [19] BiocManager_1.30.22 compiler_4.4.0 Rcpp_1.0.12
## [22] rhdf5filters_1.16.0 rhdf5_2.48.0 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