Utilities¶

prepare_svca¶

spatialtis.utils.prepare_svca(adata, export, entry_folder='svca_data', groupby=None, marker_key=None, centroid_key=None)[source]¶

Prepare data for SVCA analysis

Spatial Variance Components Analysis: SVCA

The input format is separated folder for each ROI with expressions.txt and positions.txt.

Parameters

adata – The AnnData object to process
export – The directory to store the data
entry_folder – The name of new folder to store the data
groupby – How your experiments data grouped, (Default: spatialtis.CONFIG.EXP_OBS)
marker_key – The key to store markers in AnnData.var (Default: spatialtis.CONFIG.MARKER_KEY) used in the header of the expressions.txt
centroid_key – The key to store cell centroid in AnnData.obs (Default: spatialtis.CONFIG.CENTROID_KEY)

spatialtis.utils.df2adata_uns(df, adata, key, params=None, verbose=None)[source]¶

Write pandas.DataFrame with parameters to AnnData.uns

The AnnData haven’t fully support read/write of a pandas.Dataframe object, this is a temporal solution to store it in a Dict

The meaning of each key:

df: The dataframe itself

iname: The name of index/MultiIndex

colname: The name of columns/MultiIndex

params: The parameters

Parameters

df (pandas.core.frame.DataFrame) – The pandas.DataFrame object you want to write to the AnnData.uns field
adata (anndata._core.anndata.AnnData) – The AnnData object for storage
key (str) – Which key in AnnData.obs key you want to write
params (Optional[Dict]) – Add parameters
verbose (Optional[bool]) – Control the verbosity

spatialtis.utils.adata_uns2df(adata, key, params=False)[source]¶

Read pandas.DataFrame object from AnnData.uns written by df2adata_uns

Parameters

spatialtis.utils.col2adata_obs(col, adata, key, verbose=None)[source]¶

Write an array to AnnData.obs

Parameters