Saving BumpyMatrices to file

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.

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"

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 7 rows and 2 columns
##             x         y
##     <numeric> <numeric>
##   1  0.309368  0.840747
##   2  0.150348  0.243826
##   3  0.185772  0.411491
##   4  0.726183  0.774937
##   5  0.807425  0.633823
##   6  0.552641  0.913913
##   7  0.246992  0.855256

Session info

sessionInfo()
## R version 4.5.2 (2025-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.3 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_1.11.0 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_1.51               rlang_1.1.7             
##  [4] xfun_0.55                jsonlite_2.0.0           buildtools_1.0.0        
##  [7] htmltools_0.5.9          maketools_1.3.2          sys_3.4.3               
## [10] sass_0.4.10              rmarkdown_2.30           grid_4.5.2              
## [13] evaluate_1.0.5           jquerylib_0.1.4          fastmap_1.2.0           
## [16] Rhdf5lib_1.33.0          alabaster.schemas_1.11.0 yaml_2.3.12             
## [19] IRanges_2.45.0           lifecycle_1.0.5          BiocManager_1.30.27     
## [22] compiler_4.5.2           Rcpp_1.1.0.8.2           rhdf5filters_1.23.3     
## [25] rhdf5_2.55.12            lattice_0.22-7           digest_0.6.39           
## [28] R6_2.6.1                 Matrix_1.7-4             bslib_0.9.0             
## [31] tools_4.5.2              cachem_1.1.0