Contents

1 Overview

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.

2 Saving a 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"                        "_environment.json"            
## [3] "concatenated/OBJECT"           "concatenated/basic_columns.h5"
## [5] "partitions.h5"

3 Loading a 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 6 rows and 2 columns
##             x         y
##     <numeric> <numeric>
##   1  0.642153  0.891735
##   2  0.815996  0.983277
##   3  0.624267  0.158241
##   4  0.614241  0.177918
##   5  0.145603  0.474682
##   6  0.964689  0.755817

Session info

sessionInfo()
## R Under development (unstable) (2025-11-04 r88984)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.8
## 
## Matrix products: default
## BLAS:   /System/Library/Frameworks/Accelerate.framework/Versions/A/Frameworks/vecLib.framework/Versions/A/libBLAS.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.6-arm64/Resources/lib/libRlapack.dylib;  LAPACK version 3.12.1
## 
## 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_1.11.0 alabaster.base_1.11.1  S4Vectors_0.49.0      
## [4] BiocGenerics_0.57.0    generics_0.1.4         BumpyMatrix_1.19.0    
## [7] BiocStyle_2.39.0      
## 
## loaded via a namespace (and not attached):
##  [1] cli_3.6.5                knitr_1.50               rlang_1.1.6             
##  [4] xfun_0.54                jsonlite_2.0.0           htmltools_0.5.8.1       
##  [7] sass_0.4.10              rmarkdown_2.30           grid_4.6.0              
## [10] evaluate_1.0.5           jquerylib_0.1.4          fastmap_1.2.0           
## [13] Rhdf5lib_1.33.0          alabaster.schemas_1.11.0 yaml_2.3.10             
## [16] IRanges_2.45.0           lifecycle_1.0.4          bookdown_0.45           
## [19] BiocManager_1.30.26      compiler_4.6.0           Rcpp_1.1.0              
## [22] rhdf5filters_1.23.0      rhdf5_2.55.8             lattice_0.22-7          
## [25] digest_0.6.38            R6_2.6.1                 bslib_0.9.0             
## [28] Matrix_1.7-4             tools_4.6.0              cachem_1.1.0