SpatialExperiment
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Potential new`.parquet` format for `tissue_position` of VisiumHD might trigger issues for `read10xVisium`
Thanks for creating and maintaining the package.
I'm experimenting the SpatialExperiment::read10xVisium
to import the Visium HD data via https://www.10xgenomics.com/datasets/visium-hd-cytassist-gene-expression-libraries-of-mouse-brain-he.
I noticed in this example data, specifically default Spaceranger output square_008um_outputs.tar.gz
(unzipped and outs
folder created), they changed the format for the tissue_position
file from .csv
to .parquet
.
>tree spatial
spatial
├── aligned_fiducials.jpg
├── aligned_tissue_image.jpg
├── cytassist_image.tiff
├── detected_tissue_image.jpg
├── scalefactors_json.json
├── tissue_hires_image.png
├── tissue_lowres_image.png
└── tissue_positions.parquet
This seems to both cause problem when setting names for xyz
because the function only detects .csv
files,
https://github.com/drighelli/SpatialExperiment/blob/cfd929f7310e3f85c966e7d56b661a0ba99b40b6/R/read10xVisium.R#L132-L139,
and the error reports on L139 due to xyz
is a character vector of length zero.
Error in names(xyz) <- names(sfs) <- sids :
'names' attribute [1] must be the same length as the vector [0]
Secondly, the current implementation .read_xyz
doesn't seem to be compatible to read in .parquet
file.
The parquet file may be able to be loaded via https://www.rdocumentation.org/packages/arrow/versions/0.14.1/topics/read_parquet.
Thanks!