constructor loses mainExpName and altExpNames from SCE

[LiNk-NY]

Hi Dario, @drighelli

I am using the Xenium example dataset from 10X to generate a SpatialExperiment object. I first create a SingleCellExperiment object and then pass it to the constructor.

Below I have two SpatialExperiment constructor calls. The first call does not capture all the information from the sce object. The second call is a workaround to include this information explicitly.

The expected behavior is that the SpatialExperiment constructor provide a very similar SPE (if not identical) to the latter when provided with a SingleCellExperiment object.
Unfortunately, it seems that the mainExpName, rowData, and altExpNames (and possibly the reducedDimNames) are lost when an SCE is provided to the constructor.

I think the information should be kept as is as much as possible.

Note that as(sce, "SpatialExperiment") does a good job at keeping the information in the object.

Best regards,
Marcel

## BiocManager::install("waldronlab/XeniumIO")
suppressPackageStartupMessages({
    library(XeniumIO)
    library(SpatialExperiment)
})
zipfile <- paste0(
    "https://mghp.osn.xsede.org/bir190004-bucket01/BiocXenDemo/",
    "Xenium_Prime_MultiCellSeg_Mouse_Ileum_tiny_outs.zip"
)
destfile <- XeniumIO:::.cache_url_file(zipfile)
outfold <- file.path(
    tempdir(), tools::file_path_sans_ext(basename(zipfile))
)
if (!dir.exists(outfold))
    dir.create(outfold, recursive = TRUE)
unzip(
    zipfile = destfile, exdir = outfold, overwrite = FALSE
)
con <- TENxXenium(xeniumOut = outfold)
sce <- import(con@resources)
metadata <- import(con@metadata)
coldata <- import(con@colData)

SpatialExperiment(
    sce,
    sample_id = con@sampleId,
    colData = as(coldata, "DataFrame"),
    spatialCoordsNames = con@coordNames,
    metadata = list(
        experiment.xenium = metadata,
        polygons = import(con@boundaries)
    )
)
#> class: SpatialExperiment 
#> dim: 8 36 
#> metadata(2): experiment.xenium polygons
#> assays(1): ''
#> rownames(8): DeprecatedCodeword_0321 DeprecatedCodeword_6781 ...
#>   DeprecatedCodeword_16059 DeprecatedCodeword_18533
#> rowData names(0):
#> colnames(36): aaamobki-1 aaclkaod-1 ... olbjkpjc-1 omjmdimk-1
#> colData names(13): cell_id transcript_counts ... segmentation_method
#>   sample_id
#> reducedDimNames(0):
#> mainExpName: NULL
#> altExpNames(0):
#> spatialCoords names(2) : x_centroid y_centroid
#> imgData names(0):

## mainExpName and altExpNames are lost when SCE sent to constructor
SpatialExperiment(
    assays = list(assay(sce)),
    rowData = rowData(sce),
    mainExpName = mainExpName(sce),
    altExps = altExps(sce),
    sample_id = con@sampleId,
    colData = as(coldata, "DataFrame"),
    spatialCoordsNames = con@coordNames,
    metadata = list(
        experiment.xenium = metadata,
        polygons = import(con@boundaries)
    )
)
#> class: SpatialExperiment 
#> dim: 8 36 
#> metadata(2): experiment.xenium polygons
#> assays(1): ''
#> rownames(8): DeprecatedCodeword_0321 DeprecatedCodeword_6781 ...
#>   DeprecatedCodeword_16059 DeprecatedCodeword_18533
#> rowData names(3): ID Symbol Type
#> colnames(36): aaamobki-1 aaclkaod-1 ... olbjkpjc-1 omjmdimk-1
#> colData names(13): cell_id transcript_counts ... segmentation_method
#>   sample_id
#> reducedDimNames(0):
#> mainExpName: Deprecated Codeword
#> altExpNames(5): Gene Expression Genomic Control Negative Control
#>   Codeword Negative Control Probe Unassigned Codeword
#> spatialCoords names(2) : x_centroid y_centroid
#> imgData names(0):

^{Created on 2024-12-09 with reprex v2.1.1}