spatialtis.config._Config

class spatialtis.config._Config

Global configurations for spatialtis.

Do not directly import this class, import the instance created for you.

>>> from spatialtis import Config

This allows you to set global configuration, so that you don’t have to repeatly pass the same parameters in every function.

To set a config, simple set the attribute.

>>> Config.auto_save = True  # auto save to current directory
>>> Config.auto_save = "my_spatialtis_result"  # save to custom directory

To view your current configs.

>>> Config.view()
       Current configurations of SpatialTis
┌─────────────────────────┬───────────────┬───────┐
│ Options                 │ Attributes    │ Value │
├─────────────────────────┼───────────────┼───────┤
│ Multiprocessing         │ mp            │ True  │
│ Verbose                 │ verbose       │ True  │
│ Progress bar            │ progress_bar  │ False │
│ Auto save               │ auto_save     │ False │
│ Experiment observations │ exp_obs       │ None  │
│ ROI key                 │ roi_key       │       │
│ Cell type key           │ cell_type_key │       │
│ Marker key              │ marker_key    │       │
│ Centroid key            │ centroid_key  │       │
│ Shape key               │ shape_key     │       │
└─────────────────────────┴───────────────┴───────┘

Attributes

exp_obsstr or list of str, default: None

Required. The columns in .obs that tells how your experiments organized, for example, you have different columns [‘patients’, ‘sex’, ‘organ_part’, ‘roi_id’], the last one will be used as roi_key. You can override it by setting roi_key.

centroid_keystr, default: None

Required. The column in .obs or .obsm that store cell coordination, could be array-like or wkt format.

roi_keystr, default: None

Set the roi_key.

shape_keystr, default: None

The columns in .obs that store cell shape, must be in wkt format, use spatialtis.wkt_shapes to transform you data into wkt.

cell_type_keystr, default: None

The columns in .obs that store cell type name, some analyses require cell type name to proceed.

marker_keystr, default: None

The columns in .var that store protein/gene/transcript… name, if not specific, will use .var.index.

mpbool, default: True

To turn on/off multiprocessing. From v0.5.0, this paramter has no effect.

verbosebool, default: True

Control the printed message.

progress_barbool, default True

Control the progress bar.

auto_savebool or str or path, default: False

Set to True will automatically save all images in spatialtis_result fold created at current directory, you can also pass a path to it.

Methods

dumps(data)	Save configurations to anndata
loads(data)	Load configurations from anndata
reset()	Reset to default
view()	Print a table with current configurations

dumps(data)

Save configurations to anndata

Parameters

dataAnnData

The AnnData object to save the Config

loads(data)

Load configurations from anndata

Parameters

dataAnnData

The AnnData object to load the Config

reset()

Reset to default

view()

Print a table with current configurations