alabaster.bumpy 1.2.0
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 stageObject
:
library(alabaster.bumpy)
tmp <- tempfile()
dir.create(tmp)
meta <- stageObject(mat, tmp, "bumpy")
.writeMetadata(meta, tmp)
## $type
## [1] "local"
##
## $path
## [1] "bumpy/groups.csv.gz"
list.files(file.path(tmp, "bumpy"), recursive=TRUE)
## [1] "concatenated/simple.csv.gz" "concatenated/simple.csv.gz.json"
## [3] "groups.csv.gz" "groups.csv.gz.json"
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::loadObject()
or related functions, and the R interface will automatically do the rest.
loadObject(meta, tmp)
## 5 x 4 BumpyDataFrameMatrix
## rownames: NULL
## colnames: NULL
## preview [1,1]:
## DataFrame with 4 rows and 2 columns
## x y
## <numeric> <numeric>
## 1 0.0897662 0.626096
## 2 0.5700187 0.441637
## 3 0.1597034 0.780095
## 4 0.0511926 0.477003
sessionInfo()
## R version 4.3.1 (2023-06-16)
## Platform: x86_64-pc-linux-gnu (64-bit)
## Running under: Ubuntu 22.04.3 LTS
##
## Matrix products: default
## BLAS: /home/biocbuild/bbs-3.18-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] IRanges_2.36.0 alabaster.bumpy_1.2.0 alabaster.base_1.2.0
## [4] S4Vectors_0.40.0 BiocGenerics_0.48.0 BumpyMatrix_1.10.0
## [7] BiocStyle_2.30.0
##
## loaded via a namespace (and not attached):
## [1] cli_3.6.1 knitr_1.44 rlang_1.1.1
## [4] xfun_0.40 jsonlite_1.8.7 V8_4.4.0
## [7] htmltools_0.5.6.1 sass_0.4.7 rmarkdown_2.25
## [10] grid_4.3.1 evaluate_0.22 jquerylib_0.1.4
## [13] fastmap_1.1.1 Rhdf5lib_1.24.0 alabaster.schemas_1.2.0
## [16] yaml_2.3.7 bookdown_0.36 jsonvalidate_1.3.2
## [19] BiocManager_1.30.22 compiler_4.3.1 rhdf5filters_1.14.0
## [22] Rcpp_1.0.11 rhdf5_2.46.0 lattice_0.22-5
## [25] digest_0.6.33 R6_2.5.1 curl_5.1.0
## [28] bslib_0.5.1 Matrix_1.6-1.1 tools_4.3.1
## [31] cachem_1.0.8