API

Spacemake class

Accessing spacemake objects from python

class spacemake.smk.Spacemake(root)

Spacemake.

Class to access spacemake processed data from python.

load_processed_adata(project_id, sample_id, run_mode_name, umi_cutoff)

Load spacemake processed data.

Parameters:

project_id (str) – project_id of the data to be loaded.
sample_id (str) – sample_id of the data to be loaded.
run_mode_name (str) – name of the run mode of the data to be loaded. Each sample can have several run_modes during sample addition, here only one option needs to be provided.
umi_cutoff (int) – the umi_cutoff of the data to be loaded. Each run_mode can have several umi_cutoffs provided during configuration here only one option needs to be provided.

Returns:

A spacemake processed and analyzed AnnData object, containing the results of the analysis.

Return type:

anndata.AnnData

load_raw_spatial_adata(project_id, sample_id, run_mode_name)

Load raw, spacemake processed data.

This function will load the raw countr matrix, created by spacemake.

Parameters:

project_id (str) – project_id of the raw data to be loaded.
sample_id (str) – sample_id of the raw data to be loaded.
run_mode_name (str) – name of the run mode of the raw data to be loaded. Each sample can have several run_modes during sample addition, here only one option needs to be provided.

Returns:

A spacemake processed AnnData object, containing unfiltered raw expression data, and all cells or spatial units in the dataset.

Return type:

anndata.AnnData