Input/Output

Input/Output#

sparty.io.load_cosmx(path, dataset_id='R5941_ColonTMA', feature_key='target')#

Load cosmx data as SpatialData object

Parameters:

  • path (str) – path to folder.

  • dataset_id (str (default: 'R5941_ColonTMA')) – dataset_id.

  • feature_key (str (default: 'target')) – default column for feature name in transcripts.

Return type:

SpatialData

Returns:

SpatialData object

sparty.io.load_merscope(path, slide_name, vpt_outputs=None, region_name='region_0', z_layers=2, feature_key='gene', layer='counts')#

Load vizgen merscope data as SpatialData object

Parameters:

  • path (str) – path to folder.

  • vpt_outputs (str (default: None)) – path to vpt folder.

  • region_name (str (default: 'region_0')) – region_name id.

  • slide_name (str) – slide_name id.

  • z_layers (int (default: 2)) – z layers to load.

  • feature_key (str (default: 'gene')) – default column for feature name in transcripts.

Return type:

SpatialData

Returns:

SpatialData object

sparty.io.load_xenium(path, layer='counts', region='cell_boundaries', feature_key='feature_name', instance_key='cell_id', table_key='table', spatial_key='spatial', index_table=True, n_jobs=1)#

Load xenium data as SpatialData object

Parameters:

  • path (str) – path to folder.

  • index_table (bool (default: True)) – rename the index in table.obs with the cell_id

  • region (str (default: 'cell_boundaries')) – default shape element for region in table.obs.

  • feature_key (str (default: 'feature_name')) – default column for feature name in transcripts.

  • n_jobs (int (default: 1)) – number of jobs to load the xenium object

Return type:

SpatialData

Returns:

SpatialData object

sparty.io.shapes_from_xe(file, pixel_size=0.2125, plot_fig=True, ncols=4, return_gdf=True)#

Create polygons from a CSV file containing X/Y coordinates.

If the CSV has a ‘Selection’ column, one polygon is created per selection. Otherwise, the whole file is treated as one polygon.