hest.readers.VisiumReader

class hest.readers.VisiumReader

10x Genomics Visium reader

Methods table

auto_read(path, **read_kwargs)

Automatically detect the file names and determine a reading strategy based on the detected files.

read(img_path[, filtered_bc_matrix_path, ...])

read 10x visium with its associated image

Methods

VisiumReader.auto_read(path: str, **read_kwargs) → HESTData

Automatically detect the file names and determine a reading strategy based on the detected files. For more control on the reading process, consider using read() instead

Parameters:

path (st) – path to the directory containing all the necessary files

Returns:

STObject that was read

Return type:

HESTData

VisiumReader.read(img_path: str, filtered_bc_matrix_path: str = None, raw_bc_matrix_path: str = None, spatial_coord_path: str = None, alignment_file_path: str = None, mex_path: str = None, scanpy_h5_path: str = None, metric_file_path: str = None, custom_adata: sc.AnnData = None, autoalign: bool = 'auto', save_autoalign: bool = False) → VisiumHESTData

read 10x visium with its associated image

requires a full resolution image and a gene expression file, only one of the gene expression files will be used in this order: - filtered_bc_matrix_path - raw_bc_matrix_path - mex_path - custom_adata - scanpy_h5_path

Parameters:

  • img_path (str) – path to the full resolution image

  • filtered_bc_matrix_path (str, optional) – path to the filtered_feature_bc_matrix.h5. Defaults to None.

  • raw_bc_matrix_path (str, optional) – path to the raw_feature_bc_matrix.h5. Defaults to None.

  • spatial_coord_path (str, optional) – path to the spatial/ folder containing either a tissue_positions.csv or a tissue_position_list.csv (is such folder exists). Defaults to None.

  • alignment_file_path (str, optional) – path to an alignment file (if exists). Defaults to None.

  • mex_path (str, optional) – path to a folder containing three files ending with barcode.tsv(.gz), features.tsv(.gz), matrix.mtx(.gz). Defaults to None.

  • scanpy_h5_path (str, optional) – path to a scanpy formated .h5ad. Defaults to None.

  • metric_file_path (str, optional) – path to a metrics_summary.csv file. Defaults to None.

  • custom_adata (sc.AnnData, optional) – a scanpy spatial AnnData object. Defaults to None.

  • autoalign (str, optional) –

    whenever to use an automated object detector to align the spots based on the fiducials in the full res image. Defaults to ‘auto’.

    • auto: use the autoaligner if no tissue_positions are detected in the spatial folder and if an alignment file is not passed

    • always: force autoalignment

    • never: do not use autalignment

  • save_autoalign (bool, optional) – whenever to save the autoalignment file and visualization plot in a spatial/ folder. Defaults to False.

Raises:

ValueError – on invalid arguments

Returns:

visium spatial data with spots aligned based on the provided arguments

Return type:

VisiumHESTData