NEWS.md

In pachterlab/SpatialFeatureExperiment: Integrating SpatialExperiment with Simple Features in sf

Version 1.6.1 (05/09/2024)

• readRDS converts old style SpatRasterImage to the new style
• readSelectTx and addSelectTx functions to read transcript spots from a few select genes from the parquet output of formatTxSpots or add them to an SFE object
• Added formatTxTech and addTxTech functions, basically thin wrappers of formatTxSpots and addTxSpots with presets for Vizgen, Xenium, and CosMX

Version 1.6.0 (04/29/2024)

• Changed defaults from sample_id = NULL to sample_id = 1L when dealing with 1 sample or "all" when dealing with multiple samples
• dim method for BioFormatsImage that doesn't load the image into memory
• Deal with univariate spatial results in featureData in cbind and changeSampleID
• Fixed super embarrassing bug in cbind that fails when combining more than 2 SFE objects
• Updated readXenium for XOA v2
• Updated BioFormatsImage to store affine transform info rather than converting to EBImage after transform
• Speed up affine transformation of sf geometries with sfheaders
• Coercion from Seurat to SFE
• SpatRasterImage and EBImage directly inherit from SpatRaster and Image respectively so the user no longer needs to call imgRaster every time they plots or operates on the image, which I find really annoying.
• Changed name EBImage to ExtImage to reduce confusion
• Bug fixes on image affine transformation
• Exporting some util functions: aggBboxes, getPixelSize, and imageIDs
• Read select genes as rowGeometry and add to existing rowGeometry without erasing existing genes in the same rowGeometry

Version 1.5.2 (03/04/2024)

• Added readXenium (for XOA v1)
• Added BioFormatsImage and EBImage classes to deal with Xenium OME-TIFF
• Conversion between SpatRasterImage, BioFormatsImage, and EBImage
• Overhaul of geometry operation functions for images and SFE objects for the new image classes, including bbox, crop, and affine transforms
• Don't throw error when there are no rows or columns left after [ subsetting
• cbind for multiple samples that have rowGeometry
• Rewrote df2df with the much faster sfheaders, deprecating the less efficient BPPARAM argument

Version 1.5.1 (02/02/2024)

• Added support for rowGeometry and transcript spots
• Reformat transcript spot files from Vizgen and CosMX
• Improved readVizgen for transcript spots
• Added readCosMX

Version 1.3.1 (09/22/2023)

• Refactored to remove "missing" methods for geometries, graphs, and local results.
• Changed defaults from sample_id = NULL to sample_id = "all" unless only one sample can be specified.

Version 1.2.3 (08/18/2023)

• 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.

Version 1.2.2 (07/21/2023)

• Fixed embarrassing documentation mismatch in localResults

Version 1.2.1 (04/26/2023)

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

Version 1.1.6 (04/20/2023)

• 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

Version 1.1.4 (03/02/2023)

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

Version 1.1.3 (12/20/2022)

• 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.

Version 1.0.3 (01/11/2023)

• Correctly move the geometries when there are multiple samples
• Use translate = FALSE when using localResult setter for geometries
• More helpful error messages when geometries, localResult, or spatial graphs are absent

Version 1.0.2 (12/03/2022)

• Correctly move spatialCoords in removeEmptySpace
• Preserve rownames when setting colGeometry for some of all samples

Version 1.0.0 (11/02/2022)

• First version on Bioconductor

Version 0.99.4 (09/07/2022)

• Added \code{localResults} field
• Also reimplemented some of the internals behind \code{dimGeometries}

Version 0.99.0 (02/09/2022)

• Hello world!
• For my personal record, this package was submitted to Bioconductor on July 22

pachterlab/SpatialFeatureExperiment documentation built on May 17, 2024, 12:24 a.m.