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 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"

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::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

Session info

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