TreeSummarizedExperiments
to artifacts and back againThe alabaster.treese
package implements methods to save TreeSummarizedExperiment
objects to file artifacts and load them back into R. It extends alabaster.sce,
which handles everything from the SingleCellExperiment
parent class. Check out the alabaster.base
for more details on the motivation and concepts of the
alabaster framework.
Given a TreeSummarizedExperiment, we can use
saveObject() to save it inside a staging directory:
# Mock up a TreeSE with a row tree and reference sequences.
library(TreeSummarizedExperiment)
data(tinyTree)
mat <- matrix(rpois(100, 10), ncol = 10)
rownames(mat) <- tinyTree[["tip.label"]]
colnames(mat) <- letters[1:10]
tse <- TreeSummarizedExperiment(list(counts = mat), rowTree = tinyTree)
tse[["stuff"]] <- LETTERS[1:10]
referenceSeq(tse) <- Biostrings::DNAStringSet(rep("ACGT", nrow(tse)))
tse## class: TreeSummarizedExperiment
## dim: 10 10
## metadata(0):
## assays(1): counts
## rownames(10): t2 t7 ... t5 t3
## rowData names(0):
## colnames(10): a b ... i j
## colData names(1): stuff
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowLinks: a LinkDataFrame (10 rows)
## rowTree: 1 phylo tree(s) (10 leaves)
## colLinks: NULL
## colTree: NULL
## referenceSeq: a DNAStringSet (10 sequences)# Save it into a staging directory.
library(alabaster.treese)
tmp <- tempfile()
saveObject(tse, tmp)
list.files(tmp, recursive = TRUE)## [1] "_environment.json"
## [2] "assays/0/array.h5"
## [3] "assays/0/OBJECT"
## [4] "assays/names.json"
## [5] "column_data/basic_columns.h5"
## [6] "column_data/OBJECT"
## [7] "OBJECT"
## [8] "reference_sequences/names.txt.gz"
## [9] "reference_sequences/OBJECT"
## [10] "reference_sequences/sequences.fasta.gz"
## [11] "row_data/basic_columns.h5"
## [12] "row_data/OBJECT"
## [13] "row_links/basic_columns.h5"
## [14] "row_links/OBJECT"
## [15] "row_trees/0/list_contents.h5"
## [16] "row_trees/0/OBJECT"
## [17] "row_trees/names.json"We can then load it back into the session with
readObject().
## [1] "TreeSummarizedExperiment"
## attr(,"package")
## [1] "TreeSummarizedExperiment"Each tree in rowTree() or colTree() is
saved as a list containing the fields of its phylo object,
with the edge matrix split into parent and
child vectors. We do not use Newick as it does not preserve
the node numbering (which is referenced by rowLinks() and
colLinks()) or labels containing special characters. Users
who need a Newick file for other tools can always create one with
ape::write.tree(). The links themselves are saved as data
frames, while the referenceSeq() is saved as FASTA via
alabaster.string.
## R version 4.6.1 (2026-06-24)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 26.04.1 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-r0.3.32.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=en_US.UTF-8
## [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.treese_0.99.0 alabaster.base_1.13.4
## [3] TreeSummarizedExperiment_2.21.0 Biostrings_2.81.9
## [5] XVector_0.53.0 SingleCellExperiment_1.35.2
## [7] SummarizedExperiment_1.43.0 Biobase_2.73.2
## [9] GenomicRanges_1.65.4 Seqinfo_1.3.2
## [11] IRanges_2.47.5 S4Vectors_0.51.10
## [13] BiocGenerics_0.59.12 generics_0.1.4
## [15] MatrixGenerics_1.25.0 matrixStats_1.5.0
## [17] BiocStyle_2.41.0
##
## loaded via a namespace (and not attached):
## [1] xfun_0.62 bslib_0.12.0 alabaster.string_1.13.1
## [4] rhdf5_2.57.20 lattice_0.23-1 rhdf5filters_1.25.5
## [7] vctrs_0.7.3 tools_4.6.1 yulab.utils_0.2.5
## [10] parallel_4.6.1 tibble_3.3.1 pkgconfig_2.0.3
## [13] Matrix_1.7-6 lifecycle_1.0.5 compiler_4.6.1
## [16] treeio_1.37.1 alabaster.se_1.13.1 codetools_0.2-20
## [19] htmltools_0.5.9 sys_3.4.3 buildtools_1.0.0
## [22] sass_0.4.10 alabaster.matrix_1.13.4 yaml_2.3.12
## [25] lazyeval_0.2.3 pillar_1.11.1 crayon_1.5.3
## [28] jquerylib_0.1.4 tidyr_1.3.2 BiocParallel_1.47.0
## [31] DelayedArray_0.39.8 cachem_1.1.0 abind_1.4-8
## [34] nlme_3.1-171 tidyselect_1.2.1 digest_0.6.39
## [37] dplyr_1.2.1 purrr_1.2.2 maketools_1.3.2
## [40] fastmap_1.2.0 grid_4.6.1 cli_3.6.6
## [43] SparseArray_1.13.4 magrittr_2.0.5 S4Arrays_1.13.2
## [46] h5mread_1.5.3 ape_5.8-1 rappdirs_0.3.4
## [49] rmarkdown_2.32 otel_0.2.0 HDF5Array_1.41.3
## [52] alabaster.sce_1.13.1 evaluate_1.0.5 knitr_1.52
## [55] rlang_1.3.0 Rcpp_1.1.2 glue_1.8.1
## [58] tidytree_0.4.8 BiocManager_1.30.27 alabaster.ranges_1.13.1
## [61] alabaster.schemas_1.13.0 jsonlite_2.0.0 Rhdf5lib_2.1.0
## [64] R6_2.6.1 fs_2.1.0