rename

rename ¶

rename(
    data,
    rename,
    fromColumn="phenotype",
    toColumn="phenotype_renamed",
    verbose=True,
    outputDir=None,
    sdataTable=None,
)

Relabel or merge the categories of an obs column.

Writes a new column rather than editing in place, so the original labels stay available. That matters when you want to plot broad classes and fine phenotypes side by side.

Parameters:

Name	Type	Description	Default
`data`	`(AnnData \| SpatialData \| str, required)`	The cell table. An `AnnData`, a path to an `.h5ad` file, a `SpatialData` object, or a path to a `.zarr` SpatialData store.	required
`rename`	`(dict, required)`	The mapping, keyed by the new label: `{"Tumour": ["ECAD+", "KI67+"], "Stroma": "SMA+"}`. Values may be a single label or a list of them. Categories that are not mentioned keep their existing label.	required
`fromColumn`	`str`	Column in `obs` to read.	`'phenotype'`
`toColumn`	`str`	Column in `obs` to write. Set this — the default `'phenotype_renamed'` is rarely what you want to plot from.	`'phenotype_renamed'`
`verbose`	`bool`	Print progress messages.	`True`
`outputDir`	`str`	Directory to write the updated object to. With `None` the object is returned instead.	`None`
`sdataTable`	`str`	Which `SpatialData` table to work on. Ignored for `AnnData` input, and optional when the store has exactly one table.	`None`

Returns:

Name	Type	Description
`adata`	`AnnData \| SpatialData \| None`	The updated object with `obs[toColumn]` set. `None` when `outputDir` is given.

Example

# Merge fine phenotypes into broad classes.
adata = sp.tl.rename(
    adata,
    rename={"Tumour": "ECAD+",
            "Immune": ["Treg", "NK cells", "Dendritic cells"]},
    fromColumn="phenotype",
    toColumn="broad",
)

# Give cluster numbers names.
adata = sp.tl.rename(
    adata,
    rename={"Tumour core": "0", "Stroma": "1", "Immune infiltrate": "2"},
    fromColumn="kmeans",
    toColumn="neighbourhood",
)