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  0.255011  0.178042
##   2  0.228359  0.332369
##   3  0.770520  0.981256
##   4  0.815193  0.535563
##   5  0.782200  0.979165
##   6  0.273596  0.827745

Session info

sessionInfo()
## R version 4.5.0 Patched (2025-04-21 r88169)
## Platform: aarch64-apple-darwin20
## Running under: macOS Ventura 13.7.1
## 
## Matrix products: default
## BLAS:   /Library/Frameworks/R.framework/Versions/4.5-arm64/Resources/lib/libRblas.0.dylib 
## LAPACK: /Library/Frameworks/R.framework/Versions/4.5-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_1.9.1 alabaster.base_1.9.0  S4Vectors_0.47.0     
## [4] BiocGenerics_0.55.0   generics_0.1.4        BumpyMatrix_1.17.0   
## [7] BiocStyle_2.37.0     
## 
## loaded via a namespace (and not attached):
##  [1] cli_3.6.5               knitr_1.50              rlang_1.1.6            
##  [4] xfun_0.52               jsonlite_2.0.0          htmltools_0.5.8.1      
##  [7] sass_0.4.10             rmarkdown_2.29          grid_4.5.0             
## [10] evaluate_1.0.3          jquerylib_0.1.4         fastmap_1.2.0          
## [13] Rhdf5lib_1.31.0         alabaster.schemas_1.9.0 yaml_2.3.10            
## [16] IRanges_2.43.0          lifecycle_1.0.4         bookdown_0.43          
## [19] BiocManager_1.30.25     compiler_4.5.0          Rcpp_1.0.14            
## [22] rhdf5filters_1.21.0     rhdf5_2.53.0            lattice_0.22-7         
## [25] digest_0.6.37           R6_2.6.1                bslib_0.9.0            
## [28] Matrix_1.7-3            tools_4.5.0             cachem_1.1.0