numeric coords properly when reading arrays 3145resize and tiledbsoma_upgrade_shape accessors as part of the new-shape projecttiledb_timestamp$write() and $create()axis parameter when initializing blockwise readsresize and tiledbsoma_upgrade_shape accessors as part of the new-shape projecttiledb_timestamp$write() and $create()axis parameter when initializing blockwise readsused_shape function is deprecated; shape mods are upcoming scheduled for TileDB-SOMA 1.15$reopen(mode = ) default to not flip modes; require explicit mode parameter to be passeddrop_levels to SOMAExperimentAxisQuery -> ecosystem outgestors to drop unused factor levelsreopen method available from RSeuratCommand logsSeuratCommand logs*m and *p layers from SOMAExperimentAxisQueryreopen() a public method for all TileDBObjectswrite_soma()TileDBCreateOptions to $initialize() instead of in the accessorsSeuratSOMADataFrame$shape() throw a not-yet-implemented errorSeuratObject::.CalcN() when outgesting from SOMA to Seurat$reopen() to reopen at the current timeSeuratCommand logsSeuratCommand logs*m and *p layers from SOMAExperimentAxisQueryreopen() a public method for all TileDBObjectswrite_soma()SeuratCommand logsSeuratCommand logs*m and *p layers from SOMAExperimentAxisQuerySeuratCommand logsSeuratCommand logswrite_soma()write_soma.character() to encode character vectors as SOMA arraysSOMADataFrame, SOMASparseNDArray, and SOMADenseNDArray's write() method now correctly leaves the array open in write modeSOMADataFrameSummarizedExperiment and SingleCellExperiment object to SOMAsSOMADataFrames with ordered() columnsSingleCellExperimentobs and varaxis_query() method to SOMAExperimentto_sparse_matrix() method to SOMAExperimentAxisQueryThis is the initial release of the tiledbsoma R package.
NEWS.md file to track changes to the packageTileDBGroup gains a names method to retrieve the names of group membersSOMAMeasurement and SOMAExperiment classesSOMAExperiment via the SOMAExperimentAxisQuery classTileDBArray class gained a colnames() method that returns the names of both dimensions and attributescoords and value_filter argumentscreate() method now return self rather than nothingfile:// prefixPlatformConfig and SOMATileDBContext classes to handle SOMA and TileDB configurationSOMAExperimentAxisQuery objectsSeurat objectsSOMAExperiment containing the pbmc_small dataset from the SeuratObject packageSOMACollection-based classes using the add_new_*() methods now pass through their parent context and platform configSOMAExperimentAxisQuery gained a to_sparse_matrix() method for retrieving data as a named sparse matrixSOMAExperiment gained axis_query() to construct a SOMAExperimentAxisQuery objectSOMAExperimentAxisQuery objects