Spatialfeatureexperiment

* Fixed bug when Visium graph is not added when filtered matrix from only one sample is read with read10xVisiumSFE.
* Changed the way pixels are converted to microns in Visium. Old way: use top left corner of Visium spot array to compute spacing between spots, doesn't work for filtered data when there're singleton spots. New way: Use median row/col indices, more robust when there're singletons. When spacing is used for the conversion, spot size is found to vary across datasets.
* Added saveRDS method for SFE objects, so SpatRaster images are wrapped before saving and unwrapped on the fly when they're requested.
* Fixed bug when the wrong bounding boxes are used to crop images when SFE object is subsetted and there're multiple samples.

* Fixed embarrassing documentation mismatch in localResults

* Fixed bug in .check_features and .symbol2id where "symbol" column is hard coded

* Read images as SpatRaster, in read10xVisiumSFE
* read10xVisiumSFE can also convert full resolution image pixels to microns based
on Visium spot spacing
* read10xVisiumSFE no longer transposes output from read10xVisium so the spots
would match the image by default, and to be consistent with SpatialExperiment
* Read standard Vizgen MERFISH output with readVizgen
* SpatRasterImage class inheriting from VirtualSpatialImage for SpatialExperiment compatibility
* Methods of addImg, mirrorImg, and transposeImg for SpatRasterImage and SFE
* Mirror and transpose SFE objects, operating on both geometries and images
* Images are cropped when the SFE object is cropped
* Images are also shifted when removeEmptySpace is called

* Store SFE package version in object and added SFE method of updateObject to pave way for a potential reimplementation of spatialGraphs.

* Use BiocNeighbors for k nearest neighbors and distance based neighbors, preserving distance info to avoid slow step to refind distances with sf as done in spdep.
* Added swap_rownames argument in localResult(s) getters so gene symbols from any rowData column can be used to get local results stored under Ensembl IDs.