How to SpatialFeaturePlot for Aggregated Samples?

[chancharikmitra]

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I have successfully visualized individual tissue samples with a standard output structure using SpatialFeaturePlot, but I would like to visualize multiple samples in one of Spaceranger's aggregated outputs. The output should be similar to using merge as shown in the Seurat documentation:

https://satijalab.org/seurat/articles/spatial_vignette.html

However, I don't want to do this manually for 16 different samples of course. How would I do that for the following spatial folder structure? There is one aggr_tissue_positions_list.csv for all samples in the outs folder.

[drighelli]

Hi @chancharikmitra,

thanks for this issue, but unfortunately when we implemented the read10xVisium, this kind of data was not around to be tested, so I'm not sure how to load the data with our read10xVisium...

What you can do, maybe is to load the data with seurat and then convert it to a SpatialExperiment with the code provided by Marc in this issue

[chancharikmitra]

Sorry for the late reply @drighelli. But I appreciate the pointer to that issue. I'll see if it can be of use. Thank you!