Layers.py
Here’s a detailed documentation for the Layers class in the cassiopeia/data/Layers.py file:
High-level description
The Layers class implements a data structure for storing multiple versions of mutation data for each cell in a CassiopeiaTree object. It behaves like a dictionary, allowing users to store, retrieve, and delete entries using standard dictionary operations.
Code Structure
The Layers class is a subclass of dict and is closely tied to the CassiopeiaTree class. It maintains a reference to its parent CassiopeiaTree object and stores layer data in an internal dictionary.
Symbols
Layers
Description
A class that represents a collection of character matrices, each storing a version of mutation data for cells in a CassiopeiaTree.
Inputs
| Name | Type | Description |
|---|---|---|
| parent | CassiopeiaTree | The parent CassiopeiaTree object |
| layers | Optional[Mapping] | Initial layers to populate the object |
Internal Logic
- Initializes with a reference to the parent CassiopeiaTree and an empty internal dictionary.
- If initial layers are provided, they are added to the internal dictionary.
- Implements dictionary-like methods for accessing, setting, and deleting layers.
- Provides custom string representation and iPython key completion.
repr
Description
Returns a string representation of the Layers object.
Outputs
| Name | Type | Description |
|---|---|---|
| return | str | String representation of the Layers object |
ipython_key_completions
Description
Returns a list of keys for iPython autocompletion.
Outputs
| Name | Type | Description |
|---|---|---|
| return | List[str] | List of layer keys |
copy
Description
Creates a shallow copy of the Layers object.
Outputs
| Name | Type | Description |
|---|---|---|
| return | Layers | A new Layers object with copied data |
getitem
Description
Retrieves a layer by key.
Inputs
| Name | Type | Description |
|---|---|---|
| key | str | The key of the layer to retrieve |
Outputs
| Name | Type | Description |
|---|---|---|
| return | pd.DataFrame | The requested layer data |
setitem
Description
Sets a layer with the given key and value.
Inputs
| Name | Type | Description |
|---|---|---|
| key | str | The key for the layer |
| value | pd.DataFrame | The layer data to set |
Internal Logic
- Validates the input value using the
_validate_valuemethod. - Stores the validated value in the internal dictionary.
delitem
Description
Deletes a layer with the given key.
Inputs
| Name | Type | Description |
|---|---|---|
| key | str | The key of the layer to delete |
contains
Description
Checks if a layer with the given key exists.
Inputs
| Name | Type | Description |
|---|---|---|
| key | str | The key to check for |
Outputs
| Name | Type | Description |
|---|---|---|
| return | bool | True if the key exists, False otherwise |
iter
Description
Returns an iterator over the layer keys.
Outputs
| Name | Type | Description |
|---|---|---|
| return | Iterator[str] | Iterator over layer keys |
len
Description
Returns the number of layers.
Outputs
| Name | Type | Description |
|---|---|---|
| return | int | Number of layers |
_validate_value
Description
Validates the input value for a layer.
Inputs
| Name | Type | Description |
|---|---|---|
| val | pd.DataFrame | The value to validate |
| key | str | The key associated with the value |
Outputs
| Name | Type | Description |
|---|---|---|
| return | pd.DataFrame | The validated value |
Internal Logic
- Checks if the input value has the correct number of samples (rows) compared to the parent CassiopeiaTree.
- Raises a ValueError if the shape is incorrect.
Dependencies
| Dependency | Purpose |
|---|---|
| typing | Type hinting |
| pandas | DataFrame operations |
| cassiopeia.data.CassiopeiaTree | Parent class reference |
This Layers class provides a flexible way to store and manage multiple versions of mutation data for cells in a CassiopeiaTree object, allowing for easy experimentation with different data representations or imputations.