LoomExperiment classThe LoomExperiment family of classes inherits from the
main class LoomExperiment as well as the Experiment class
that they are named after. For example, the
SingleCellLoomExperiment class inherits from both
LoomExperiment and SingleCellExperiment.
The purpose of the LoomExperiment class is to act as an
intermediary between Bioconductor’s Experiment classes and the Linnarson
Lab’s Loom File Format (http://linnarssonlab.org/loompy/index.html). The Loom
File Format uses HDF5 to store Experiment data.
The LoomExperiment family of classes contain the
following slots.
colGraphsrowGraphsBoth of these slots are LoomGraphs objects that describe
the col_graph and row_graph attributes as
specified by the Loom File Format.
There are several ways to create instances of a
LoomExperiment class of object. One can plug an existing
SummarizedExperiment type class into the appropriate constructor:
library(LoomExperiment)
counts <- matrix(rpois(100, lambda = 10), ncol=10, nrow=10)
sce <- SingleCellExperiment(assays = list(counts = counts))
scle <- SingleCellLoomExperiment(sce)
## OR
scle <- LoomExperiment(sce)One can also simply plug the arguments into the appropriate
constructor, since all LoomExperiment constructors call the
applicable class’s constructor
Also, it is also possible to create a LoomExperiment
extending class via coercion:
## class: SingleCellLoomExperiment
## dim: 10 10
## metadata(0):
## assays(1): counts
## rownames: NULL
## rowData names(0):
## colnames: NULL
## colData names(0):
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowGraphs(0): NULL
## colGraphs(0): NULLFinally, one can create a LoomExperiment object from
importing a Loom File.
We will use the following SingleCellLoomExperiment for
the remainder of the vignette.
l1_file <-
system.file("extdata", "L1_DRG_20_example.loom", package = "LoomExperiment")
scle <- import(l1_file, type="SingleCellLoomExperiment")
scle## class: SingleCellLoomExperiment
## dim: 20 20
## metadata(4): CreatedWith LOOM_SPEC_VERSION LoomExperiment-class
## MatrixName
## assays(1): matrix
## rownames: NULL
## rowData names(7): Accession Gene ... X_Total X_Valid
## colnames: NULL
## colData names(103): Age AnalysisPool ... cDNA_Lib_Ok ngperul_cDNA
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowGraphs(0): NULL
## colGraphs(2): KNN MKNNAll the following methods apply to all LoomExperiment
classes.
LoomGraph classThe colGraphs and rowGraphs slots of
LoomExperiments correspond to the col_graphs and
row_graphs fields in the Loom File format. Both of these
slots require LoomGraphs objects.
A LoomGraph class extends the SelfHits
class from the S4Vectors package with the requirements that
a LoomGraph object must:
integer and
non-negativeLoomExperiment object (if attached to a
LoomExperiment object)The columns to and from correspond to
either row or col indices in the
LoomExperiment object while w is an optional
column that specifies the weight.
A LoomGraph can be constructed in two ways:
a <- c(1, 2, 3)
b <- c(3, 2, 1)
w <- c(100, 10, 1)
df <- DataFrame(a, b, w)
lg <- as(df, "LoomGraph")
## OR
lg <- LoomGraph(a, b, weight = w)
lg## LoomGraph object with 3 hits and 1 metadata column:
## from to | w
## <integer> <integer> | <numeric>
## [1] 1 3 | 100
## [2] 2 2 | 10
## [3] 3 1 | 1
## -------
## nnode: 3LoomGraph objects can be subset by the ‘row’/‘col’
indices.
## LoomGraph object with 2 hits and 1 metadata column:
## from to | w
## <integer> <integer> | <numeric>
## [1] 1 3 | 100
## [2] 2 2 | 10
## -------
## nnode: 3## LoomGraph object with 2 hits and 1 metadata column:
## from to | w
## <integer> <integer> | <numeric>
## [1] 1 3 | 100
## [2] 3 1 | 1
## -------
## nnode: 3LoomGraphs classA LoomGraphs object extends the
S4Vectors:SimpleList object. It contains multiple
LoomGraph objects with its only requirement being that it
must contain LoomGraph objects.
It can be created simply by using LoomGraph objects in
the LoomGraphs constructor
## LoomGraphs of length 2
## names(2): lg1 lg2LoomExperimentThe LoomGraphs assigned to these colGraphs
and rowGraphs slots can be obtained by their eponymous
methods:
## LoomGraphs of length 2
## names(2): KNN MKNN## LoomGraphs of length 0The same symbols can also be used to replace the respective
LoomGraphs
## LoomGraphs of length 2
## names(2): lg1 lg2## LoomGraphs of length 2
## names(2): lg1 lg2## LoomGraph object with 3 hits and 1 metadata column:
## from to | w
## <integer> <integer> | <numeric>
## [1] 1 3 | 100
## [2] 2 2 | 10
## [3] 3 1 | 1
## -------
## nnode: 20## LoomGraph object with 3 hits and 1 metadata column:
## from to | w
## <integer> <integer> | <numeric>
## [1] 1 3 | 100
## [2] 2 2 | 10
## [3] 3 1 | 1
## -------
## nnode: 20LoomExperiment objects can be subsetting in such a way
that the assays, colGraphs, and
rowGraphs will all be subsetted. assays will
will be subsetted as any matrix would. The i
element in the subsetting operation will subset the
rowGraphs slot and the j element in the
subsetting operation will subset the colGraphs slot, as
we’ve seen from the subsetting method from LoomGraphs.
## LoomGraph object with 1 hit and 1 metadata column:
## from to | w
## <integer> <integer> | <numeric>
## [1] 2 2 | 10
## -------
## nnode: 2## LoomGraph object with 2 hits and 1 metadata column:
## from to | w
## <integer> <integer> | <numeric>
## [1] 1 2 | 100
## [2] 2 1 | 1
## -------
## nnode: 2## class: SingleCellLoomExperiment
## dim: 40 20
## metadata(8): CreatedWith LOOM_SPEC_VERSION ... LoomExperiment-class
## MatrixName
## assays(1): matrix
## rownames: NULL
## rowData names(7): Accession Gene ... X_Total X_Valid
## colnames: NULL
## colData names(103): Age AnalysisPool ... cDNA_Lib_Ok ngperul_cDNA
## reducedDimNames(0):
## mainExpName: NULL
## altExpNames(0):
## rowGraphs(2): lg1 lg2
## colGraphs(4): lg1 lg2 lg1 lg2## LoomGraphs of length 4
## names(4): lg1 lg2 lg1 lg2## LoomGraphs of length 2
## names(2): lg1 lg2## LoomGraph object with 3 hits and 1 metadata column:
## from to | w
## <integer> <integer> | <numeric>
## [1] 1 3 | 100
## [2] 2 2 | 10
## [3] 3 1 | 1
## -------
## nnode: 20## LoomGraph object with 6 hits and 1 metadata column:
## from to | w
## <integer> <integer> | <numeric>
## [1] 1 3 | 100
## [2] 2 2 | 10
## [3] 3 1 | 1
## [4] 21 23 | 100
## [5] 22 22 | 10
## [6] 23 21 | 1
## -------
## nnode: 40Finally, the LoomExperiment object can be exported.
## R version 4.4.2 (2024-10-31)
## Platform: x86_64-pc-linux-gnu
## Running under: Ubuntu 24.04.1 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-r0.3.26.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] LoomExperiment_1.25.0 BiocIO_1.17.1
## [3] rhdf5_2.51.0 SingleCellExperiment_1.29.1
## [5] SummarizedExperiment_1.37.0 Biobase_2.67.0
## [7] GenomicRanges_1.59.1 GenomeInfoDb_1.43.2
## [9] IRanges_2.41.1 MatrixGenerics_1.19.0
## [11] matrixStats_1.4.1 S4Vectors_0.45.2
## [13] BiocGenerics_0.53.3 generics_0.1.3
## [15] BiocStyle_2.35.0
##
## loaded via a namespace (and not attached):
## [1] sass_0.4.9 SparseArray_1.7.2 stringi_1.8.4
## [4] lattice_0.22-6 magrittr_2.0.3 digest_0.6.37
## [7] evaluate_1.0.1 grid_4.4.2 fastmap_1.2.0
## [10] jsonlite_1.8.9 Matrix_1.7-1 BiocManager_1.30.25
## [13] httr_1.4.7 UCSC.utils_1.3.0 HDF5Array_1.35.1
## [16] jquerylib_0.1.4 abind_1.4-8 cli_3.6.3
## [19] rlang_1.1.4 crayon_1.5.3 XVector_0.47.0
## [22] cachem_1.1.0 DelayedArray_0.33.2 yaml_2.3.10
## [25] S4Arrays_1.7.1 tools_4.4.2 Rhdf5lib_1.29.0
## [28] GenomeInfoDbData_1.2.13 buildtools_1.0.0 R6_2.5.1
## [31] lifecycle_1.0.4 zlibbioc_1.52.0 stringr_1.5.1
## [34] bslib_0.8.0 glue_1.8.0 xfun_0.49
## [37] sys_3.4.3 knitr_1.49 rhdf5filters_1.19.0
## [40] htmltools_0.5.8.1 rmarkdown_2.29 maketools_1.3.1
## [43] compiler_4.4.2