Issues when creating Visium HD object

[boyiguo1]

Thanks for creating the package.

I'm experimenting with VisiumIO 0.99.3 to create SpatialExperiment object for Visium HD data.

The dataset that I'm experimenting right now comes from https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-mouse-brain-he.

The first issue I had is to directly load an .tar.gz object directly via the resource statement.

spe <- TENxVisium(
     resources = "Visium_HD_Mouse_Brain_square_008um_outputs.tar.gz"
    )
Error in TENxVisium(resources = "Visium_HD_Mouse_Brain_square_008um_outputs.tar.gz") : 
  argument "spatialResource" is missing, with no default

I read from the vignette resources = "path/to/10x/visium/file.tar.gz", which I thought .tar.gz is an accepted format, can you clarify?

The second issue I had is with import function after creating an "TENxVisium" object. Specifically, I unzipped the tar.gz object to a folder (which contains a layer of outs to contain all necessary files). I was successfully running TENxVisium function. However, when I tried to import as an spe object, I received the error message Error in if (is.url) { : the condition has length > 1, which doesn't seem to come from SpatialExperiment object.

 spe <- TENxVisium(
  spacerangerOut = "square_008um",
  # spatialResource = "square_008um/spatial",
  jsonFile = "scalefactors_json.json",
  tissuePattern = "tissue_positions.parquet"
)

> spe
An object of class "TENxVisium"
Slot "resources":
TENxFileList of length 3
names(3): barcodes.tsv.gz features.tsv.gz matrix.mtx.gz

Slot "spatialList":
TENxSpatialList of length 8
names(8): aligned_fiducials.jpg ... tissue_positions.parquet

Slot "coordNames":
[1] "pxl_col_in_fullres" "pxl_row_in_fullres"

Slot "sampleId":
[1] "sample01"

> import(spe)
Error in if (is.url) { : the condition has length > 1

Here is the session info

─ Session info ─────────────────────────────────────────────────────────────────────
 setting  value
 version  R Under development (unstable) (2023-11-13 r85520)
 os       Rocky Linux 9.2 (Blue Onyx)
 system   x86_64, linux-gnu
 ui       X11
 language (EN)
 collate  en_US.UTF-8
 ctype    en_US.UTF-8
 tz       US/Eastern
 date     2024-04-14
 pandoc   3.1.3 @ /jhpce/shared/community/core/conda_R/devel/bin/pandoc

─ Packages ─────────────────────────────────────────────────────────────────────────
 package              * version   date (UTC) lib source
 abind                  1.4-5     2016-07-21 [2] CRAN (R 4.4.0)
 beachmat               2.19.1    2024-01-22 [2] Bioconductor 3.19 (R 4.4.0)
 Biobase              * 2.63.1    2024-03-29 [1] Bioconductor 3.19 (R 4.4.0)
 BiocBaseUtils          1.5.0     2023-10-24 [2] Bioconductor
 BiocGenerics         * 0.49.1    2023-11-01 [2] Bioconductor
 BiocIO                 1.13.0    2023-10-24 [2] Bioconductor
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 SparseArray            1.3.5     2024-04-09 [1] Bioconductor 3.19 (R 4.4.0)
 sparseMatrixStats      1.15.0    2023-10-24 [2] Bioconductor
 SpatialExperiment    * 1.13.2    2024-04-05 [1] Bioconductor 3.19 (R 4.4.0)
 statmod                1.5.0     2023-01-06 [2] CRAN (R 4.4.0)
 SummarizedExperiment * 1.33.3    2024-01-23 [2] Bioconductor 3.19 (R 4.4.0)
 TENxIO               * 1.5.3     2023-11-21 [1] Bioconductor 3.19 (R 4.4.0)
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 VisiumIO             * 0.99.3    2024-01-26 [1] Bioconductor 3.19 (R 4.4.0)
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[alikhuseynov]

Does this package support reading VisiumHD? @boyiguo1 as on your issue with SPE https://github.com/drighelli/SpatialExperiment/issues/150 if you need to make SPE object for VisiumHD try this function https://github.com/pachterlab/SpatialFeatureExperiment/blob/devel/R/read.R#L223-L324 I haven't PR that to SPE yet.

[alikhuseynov]

@lwaldron any updates on VisiumHD reader?

[LiNk-NY]

Hi @boyiguo1 and @alikhuseynov I just saw your message. The Visium HD format is not supported yet. I am currently working on it.

[LiNk-NY]

@boyiguo1 @alikhuseynov Visium HD format should be supported now. You can test on Bioc-devel version 3.20. Best, Marcel