smftools.tools.general_tools

smftools.tools.general_tools#

Functions

combine_layers(adata, input_layers, output_layer)

Combine layers into a single coded layer.

create_nan_mask_from_X(adata[, new_layer_name])

Generate a NaN mask layer from adata.X.

create_nan_or_non_gpc_mask(adata, obs_column)

Generate a mask layer combining NaNs and non-GpC positions.
smftools.tools.general_tools.create_nan_mask_from_X(adata, new_layer_name='nan_mask')#

Generate a NaN mask layer from adata.X.

Parameters:

  • adata (AnnData) -- AnnData object.

  • new_layer_name (str (default: 'nan_mask')) -- Name of the output mask layer.

Returns:

Updated AnnData object.

Return type:

anndata.AnnData

smftools.tools.general_tools.create_nan_or_non_gpc_mask(adata, obs_column, new_layer_name='nan_or_non_gpc_mask')#

Generate a mask layer combining NaNs and non-GpC positions.

Parameters:

  • adata (AnnData) -- AnnData object.

  • obs_column (str) -- Obs column used to derive reference-specific GpC masks.

  • new_layer_name (str (default: 'nan_or_non_gpc_mask')) -- Name of the output mask layer.

Returns:

Updated AnnData object.

Return type:

anndata.AnnData

smftools.tools.general_tools.combine_layers(adata, input_layers, output_layer, negative_mask=None, values=None, binary_mode=False)#

Combine layers into a single coded layer.

Parameters:

  • adata (AnnData) -- AnnData object.

  • input_layers (Sequence[str]) -- Input layer names.

  • output_layer (str) -- Name of the output layer.

  • negative_mask (str | None (default: None)) -- Optional binary mask layer to enforce zeros.

  • values (Optional[Sequence[int]] (default: None)) -- Values assigned to each input layer when binary_mode is False.

  • binary_mode (bool (default: False)) -- Whether to build a simple 0/1 mask.

Returns:

Updated AnnData object.

Return type:

anndata.AnnData