spateo.io.slideseq#

IO functions for Slide-seq technology.

Module Contents#

Functions#

read_slideseq_as_dataframe(→ pandas.DataFrame)

Read a Slide-seq digital expression matrix as long-format pandas DataFrame.

read_slideseq_beads_as_dataframe(→ pandas.DataFrame)

Read a Slide-seq bead locations file.

read_slideseq(→ anndata.AnnData)

Read Slide-seq data as AnnData.

Attributes#

VERSIONS

spateo.io.slideseq.VERSIONS[source]#
spateo.io.slideseq.read_slideseq_as_dataframe(path: str) → pandas.DataFrame[source]#

Read a Slide-seq digital expression matrix as long-format pandas DataFrame.

Parameters:
path

Path to file

Returns:

Pandas DataFrame with the the following standardized column names.

  • barcode: Bead barcode

  • gene: Gene name/ID

  • count: Observed UMIs. Zeros are filtered.

spateo.io.slideseq.read_slideseq_beads_as_dataframe(path: str) → pandas.DataFrame[source]#

Read a Slide-seq bead locations file.

Parameters:
path

Path to file

Returns:

Pandas DataFrame with the following columns.

  • barcode: Bead barcode

  • x, y: X, Y coordinates

spateo.io.slideseq.read_slideseq(path: str, beads_path: str, binsize: int | None = None, version: typing_extensions.Literal[slide2] = 'slide2') → anndata.AnnData[source]#

Read Slide-seq data as AnnData.

Parameters:
path

Path to Slide-seq digital expression matrix CSV.

beads_path

Path to CSV file containing bead locations.

binsize

Size of pixel bins.

version

Slideseq technology version. Currently only used to set the scale and scale units of each unit coordinate. This may change in the future.