spatialData deprecation and missing 'outs/' directory

[lmweber]

Hi @lcolladotor , this pull request has 2 updates:

• Deprecation of spatialData in the latest version of SpatialExperiment (version 1.5.2). We have moved the contents of spatialData into colData for new objects built with SPE version 1.5.2 onwards, so it is best if we update spatialLIBD to access colData instead of spatialData (e.g. for in_tissue and other similar columns). We have ensured backward compatibility in SPE so the spatialData() accessor still works for earlier objects, so existing analysis code should still work, but new objects built with SPE version 1.5.2 onwards will no longer have anything in spatialData.

• Missing outs/ directories in vignette. We had some earlier changes a few months ago regarding whether or not the outs/ directory needs to be manually added when loading 10x Genomics Visium objects. When I ran checks there were some problems in one of the vignettes due to this, so these updates fix this and the checks pass again.

The main reason for this pull request is so that we can deploy shiny apps with SPE objects built with SPE version 1.5.2 onwards.

Note this only affects Bioc-devel, not Bioc-release.

[lmweber]

I think checks are failing because it has used the old version of SpatialExperiment (version 1.4.0 instead of 1.5.2).

Maybe GitHub Actions is using Bioc-release instead of Bioc-devel.

[lmweber]

My local checks with SpatialExperiment version 1.5.2 all passed.