NEWS

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SpatialExperiment 1.11.2 (2023-09-01)

• move DropletUtils package to Suggests

SpatialExperiment 1.11.1 (2023-08-21)

• add methods to rotate/mirror spatial coordinates and objects

SpatialExperiment 1.9.5 (2023-03-02)

• bugfix for tissue positions read in incorrect order with read10xVisium() in datasets with multiple samples (bug introduced in version 1.7.1)

SpatialExperiment 1.7.2 (2022-10-07)

• support for seeing colData names with $ in RStudio

SpatialExperiment 1.7.1 (2022-07-29)

• support for reading Space Ranger V2 outputs with read10xVisium()

SpatialExperiment 1.5.3 (2022-02-28)

• rename SpatialImage class to VirtualSpatialImage

SpatialExperiment 1.5.2 (2022-01-09)

• relocate and deprecate spatialData/Names

SpatialExperiment 1.5.1 (2021-12-15)

• improved coercion methods from SingleCellExperiment to SpatialExperiment
• add new methods for image rotation/mirroring
• add path argument to imgSource()
• user flexibility whether to provide outs/ directory in read10xVisium()
• documentation updates in show methods
• additional documentation updates
• update title and description in DESCRIPTION

SpatialExperiment 1.3.2 (2021-07-27)

• spatialData moved from colData to int_colData
• restructuring of vignette and added imgData section

SpatialExperiment 1.1.700 (2021-05-05)

• updating roles in DESCRIPTION file
• adding GeneExpression biocVie
• switching LazyData to false
• fixing return value in show method documentation

SpatialExperiment 1.1.434 (2021-26-02)

• fixing subset method according to SummarizedExperiment generic definition

SpatialExperiment 1.1.432 (2021-15-02)

• fixing documentation on latex errors

SpatialExperiment 1.1.430-1.1.431 (2021-12-02)

• adding BumpyMatrix as suggests
• update documentation

SpatialExperiment 1.1.429 (2021-12-02)

• adding cd_keep = TRUE binds all the colData to the spatialData
• fixing bug for cd_keep with multiple elements

SpatialExperiment 1.1.428 (2021-12-02)

• adding itemize to assays vignette item
• correcting typo cd_keep->cd_bind in spatialData documentation

SpatialExperiment 1.1.427 (2021-09-02)

• fixing tenx vignette

SpatialExperiment 1.1.426 (2021-09-02)

• fixing read10xVisium example with data parameter

SpatialExperiment 1.1.425 (2021-08-02)

• restoring data parameter in read10xVisium
• missing itemize in combine documentation

SpatialExperiment 1.1.424 (2021-07-02)

• cleaning documentation
• removing spatialImage-methods.R file

SpatialExperiment 1.1.423 (2021-02-02)

• fixing documentation issues on imgData

SpatialExperiment 1.1.422 (2021-29-01)

• removing ve data because of local image problem (using example(read10xVisium) instead)

SpatialExperiment 1.1.421 (2021-28-01)

• fixing ve data local image problem

SpatialExperiment 1.1.42 (2021-21-01)

• implementing new SpatialExperiment class
• spatialData slot
• imgData and image handling methods (HLC)

SpatialExperiment 1.1.6 (2021-02-04)

• removed additional slots in the SPE class definition (i.e. spatialData and spatialCoordsNames)
• spatialCoords stored in int_colData() = numeric matrix
• spatialDataNames stored in int_metadata() = character vector specifying a subset of colData()
• the SPE show method does not include spatialData in colData; instead, spatialData/CoordNames are printed separately
• the SPE constructor now allows specification of spatialData/Coords/-Names where -Names can be a subset of the supplied colData(); spatialData/Coords are thus optional
• cbind() now allows duplicated sample_ids, which are made unique with a message
• consistent usage of "spe" for SpatialExperiment objects across all examples (previously, both ve and se were used as well)
• fixed cache/path-related error on windows in SpatialImage unit tests
• added unit-tests of SpatialExperiment class validity
• imgData field in int_metadata is now required to exist (but can be an empty DFrame)
• colData<- protects sample_id & spatialDataNames fields; spatialData<- protects colData

SpatialExperiment 1.1.5 (2021-31-03)

• version bump to x.y.z format with .z increment
• general code-style revision to keep to Bioc guidelines including, e.g.
• usage of accessors (and not @)
• keeping to a 80-character limit
• spaces around logical operators (but not function arguments)
• in-line { for function definitions, if-else statements etc.
• re-ordering of roxygen2 documentation to be consistent across scripts

SpatialExperiment 0.99.4 (2020-24-07)

• implementing bioconductor revisions first round

SpatialExperiment 0.99.3 (2020-21-07)

• implementing imagePaths in VisiumExperiment class
• SpatialExperiment can now be created also without spatial coordinates

SpatialExperiment 0.99.2 (2020-17-07)

• adding version 0.99.2

SpatialExperiment 0.99.1 (2020-09-07)

• adding version 0.99.1