I installed SingleCellExperiment_1.12.0.

I am unable to store records in the SingleCellExperiment reduceDims metadata slot using accessors; that is, I want to store the information in

...
  ..@ int_colData        :Formal class 'DFrame' [package "S4Vectors"] with 6 slots
  .. .. ..@ rownames       : NULL
  .. .. ..@ nrows          : int 0
  .. .. ..@ listData       :List of 3
  .. .. .. ..$ reducedDims:Formal class 'DFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. .. ..@ nrows          : int 0
  .. .. .. .. .. ..@ listData       : Named list()
  .. .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. ..@ metadata       : list()   <----------------------------------------- here
  .. .. .. ..$ altExps    :Formal class 'DFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. .. ..@ nrows          : int 0
  .. .. .. .. .. ..@ listData       : Named list()
  .. .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. ..@ metadata       : list()
  .. .. .. ..$ colPairs   :Formal class 'DFrame' [package "S4Vectors"] with 6 slots
  .. .. .. .. .. ..@ rownames       : NULL
  .. .. .. .. .. ..@ nrows          : int 0
  .. .. .. .. .. ..@ listData       : Named list()
  .. .. .. .. .. ..@ elementType    : chr "ANY"
  .. .. .. .. .. ..@ elementMetadata: NULL
  .. .. .. .. .. ..@ metadata       : list()
  .. .. ..@ elementType    : chr "ANY"
  .. .. ..@ elementMetadata: NULL
  .. .. ..@ metadata       : list()
...

== I try to store information using

> library(SingleCellExperiment)
> sce<-SingleCellExperiment()
> str(reducedDims(sce))
Formal class 'SimpleList' [package "S4Vectors"] with 4 slots
  ..@ listData       : Named list()
  ..@ elementType    : chr "ANY"
  ..@ elementMetadata: NULL
  ..@ metadata       : list()
> metadata(reducedDims(sce))[['e_a']] <- 'a'
> str(metadata(reducedDims(sce))[['e_a']])
 NULL
> str(metadata(reducedDims(sce)))
 list()

== I can sneak information in directly

> sce@int_colData@listData$reducedDims@metadata[['e_a']] <- 'a'
> metadata(reducedDims(sce))
$e_a
[1] "a"

== The following fails too

> sce <- SingleCellExperiment()
> reducedDims(sce)@metadata[['e_a']] <- 'a'
> str(reducedDims(sce))
Formal class 'SimpleList' [package "S4Vectors"] with 4 slots
  ..@ listData       : Named list()
  ..@ elementType    : chr "ANY"
  ..@ elementMetadata: NULL
  ..@ metadata       : list()
> str(metadata(reducedDims(sce)))
 list()

I wonder how I am erring.

I re-installed Bioconductor 3.12 as a precaution.

> BiocManager::version()
[1] ‘3.12’

The sessionInfo is

> sessionInfo()
R version 4.0.3 (2020-10-10)
Platform: x86_64-pc-linux-gnu (64-bit)
Running under: Debian GNU/Linux 10 (buster)

Matrix products: default
BLAS:   /usr/lib/x86_64-linux-gnu/blas/libblas.so.3.8.0
LAPACK: /usr/lib/x86_64-linux-gnu/lapack/liblapack.so.3.8.0

locale:
 [1] LC_CTYPE=en_US.UTF-8       LC_NUMERIC=C               LC_TIME=en_US.UTF-8        LC_COLLATE=en_US.UTF-8     LC_MONETARY=en_US.UTF-8    LC_MESSAGES=en_US.UTF-8
 [7] LC_PAPER=en_US.UTF-8       LC_NAME=C                  LC_ADDRESS=C               LC_TELEPHONE=C             LC_MEASUREMENT=en_US.UTF-8 LC_IDENTIFICATION=C

attached base packages:
[1] parallel  stats4    stats     graphics  grDevices utils     datasets  methods   base

other attached packages:
 [1] SingleCellExperiment_1.12.0 SummarizedExperiment_1.20.0 Biobase_2.50.0              GenomicRanges_1.42.0        GenomeInfoDb_1.26.2         IRanges_2.24.1
 [7] S4Vectors_0.28.1            BiocGenerics_0.36.0         MatrixGenerics_1.2.0        matrixStats_0.57.0

loaded via a namespace (and not attached):
 [1] lattice_0.20-41        bitops_1.0-6           grid_4.0.3             zlibbioc_1.36.0        XVector_0.30.0         Matrix_1.3-2           tools_4.0.3
 [8] RCurl_1.98-1.2         DelayedArray_0.16.1    compiler_4.0.3         GenomeInfoDbData_1.2.4

Thank you.

There is the current easy way, and the future hard way.

The easy way

Store extra bits and pieces in the attributes of the matrix.

mat <- matrix(runif(100), ncol=2)
attr(mat, "stuff") <- list(A=1, B=2)

This is nice and simple, and the resulting object is still a matrix that is compatible with all downstream functions. It's also pretty clear how to get information out:

attr(mat, "stuff")$A
## [1] 1

The biggest downside is that subsetting the matrix will drop all of the (non-dimension-related) attributes. So if you put this in the reducedDims and then subset the SCE, the attributes are gone. Maybe this is a problem, maybe not.

The hard way

Well, it's not that hard, it just doesn't exist yet.

The modification is relatively simple and involves respecting any mcols() passed to reducedDims<-() if a List is supplied as the value. The key point is to use mcols() instead of metadata() - this allows us to link each piece of metadata to its associated dimensionality reduction entry, such that removing the latter will also remove the former. For example:

library(S4Vectors)
x <- List(PCA=matrix(runif(10), ncol=2), UMAP=matrix(runif(10), ncol=2))
mcols(x)$info <- list(PCA=list(rotation=1), UMAP=list(other="stuff"))

sub <- x[2]
mcols(sub)$info
## $UMAP
## $UMAP$other
## [1] "stuff"

You can see how the PCA's information was automatically removed, so it's not sticking around and confusing people when there isn't a PCA result in the list. The advantage of this approach is that it is robust to subsetting of the SCE, as the extra pieces of information will not be dropped like the attributes are. The problem is that it's a little less obvious about how to store and retrieve this information.

If you are interested in the second approach, raise an issue on the GitHub repository and we'll think about how to implement it.