Changes in version 1.15.2 (2024-06-21) o deprecation of read10xVisium() in favor of VisiumIO's TENxVisiumList() Changes in version 1.15.1 (2024-06-20) o bug fix (#151): getImg now handles non-character sample and image IDs Changes in version 1.15.0 (2024-05-01) o Bioconductor 3.19 release Changes in version 1.11.2 (2023-09-01) o move DropletUtils package to Suggests Changes in version 1.11.1 (2023-08-21) o add methods to rotate/mirror spatial coordinates and objects Changes in version 1.9.5 (2023-03-02) o bugfix for tissue positions read in incorrect order with read10xVisium() in datasets with multiple samples (bug introduced in version 1.7.1) Changes in version 1.7.2 (2022-10-07) o support for seeing colData names with $ in RStudio Changes in version 1.7.1 (2022-07-29) o support for reading Space Ranger V2 outputs with read10xVisium() Changes in version 1.5.3 (2022-02-28) o rename SpatialImage class to VirtualSpatialImage Changes in version 1.5.2 (2022-01-09) o relocate and deprecate spatialData/Names Changes in version 1.5.1 (2021-12-15) o improved coercion methods from SingleCellExperiment to SpatialExperiment o add new methods for image rotation/mirroring o add path argument to imgSource() o user flexibility whether to provide outs/ directory in read10xVisium() o documentation updates in show methods o additional documentation updates o update title and description in DESCRIPTION Changes in version 1.3.2 (2021-07-27) o spatialData moved from colData to int_colData o restructuring of vignette and added imgData section Changes in version 1.1.700 (2021-05-05) o updating roles in DESCRIPTION file o adding GeneExpression biocVie o switching LazyData to false o fixing return value in show method documentation Changes in version 1.1.434 (2021-26-02) o fixing subset method according to SummarizedExperiment generic definition Changes in version 1.1.432 (2021-15-02) o fixing documentation on latex errors Changes in version 1.1.430-1.1.431 (2021-12-02) o adding BumpyMatrix as suggests o update documentation Changes in version 1.1.429 (2021-12-02) o adding cd_keep = TRUE binds all the colData to the spatialData o fixing bug for cd_keep with multiple elements Changes in version 1.1.428 (2021-12-02) o adding itemize to assays vignette item o correcting typo cd_keep->cd_bind in spatialData documentation Changes in version 1.1.427 (2021-09-02) o fixing tenx vignette Changes in version 1.1.426 (2021-09-02) o fixing read10xVisium example with data parameter Changes in version 1.1.425 (2021-08-02) o restoring data parameter in read10xVisium o missing itemize in combine documentation Changes in version 1.1.424 (2021-07-02) o cleaning documentation o removing spatialImage-methods.R file Changes in version 1.1.423 (2021-02-02) o fixing documentation issues on imgData Changes in version 1.1.422 (2021-29-01) o removing ve data because of local image problem (using example(read10xVisium) instead) Changes in version 1.1.421 (2021-28-01) o fixing ve data local image problem Changes in version 1.1.42 (2021-21-01) o implementing new SpatialExperiment class o spatialData slot o imgData and image handling methods (HLC) Changes in version 1.1.6 (2021-02-04) o removed additional slots in the SPE class definition (i.e. spatialData and spatialCoordsNames) o spatialCoords stored in int_colData() = numeric matrix o spatialDataNames stored in int_metadata() = character vector specifying a subset of colData() o the SPE show method does not include spatialData in colData; instead, spatialData/CoordNames are printed separately o 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 o cbind() now allows duplicated sample_ids, which are made unique with a message o consistent usage of "spe" for SpatialExperiment objects across all examples (previously, both ve and se were used as well) o fixed cache/path-related error on windows in SpatialImage unit tests o added unit-tests of SpatialExperiment class validity o imgData field in int_metadata is now required to exist (but can be an empty DFrame) o colData<- protects sample_id & spatialDataNames fields; spatialData<- protects colData Changes in version 1.1.5 (2021-31-03) o version bump to x.y.z format with .z increment o general code-style revision to keep to Bioc guidelines including, e.g. o usage of accessors (and not @) o keeping to a 80-character limit o spaces around logical operators (but not function arguments) o in-line { for function definitions, if-else statements etc. o re-ordering of roxygen2 documentation to be consistent across scripts Changes in version 0.99.4 (2020-24-07) o implementing bioconductor revisions first round Changes in version 0.99.3 (2020-21-07) o implementing imagePaths in VisiumExperiment class o SpatialExperiment can now be created also without spatial coordinates Changes in version 0.99.2 (2020-17-07) o adding version 0.99.2 Changes in version 0.99.1 (2020-09-07) o adding version 0.99.1