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Replace refitted values

replace_refitted_values

ReplaceRefittedValues

Mixin class to replace refitted values.

Source code in fedpydeseq2/core/deseq2_core/replace_refitted_values/replace_refitted_values.py 
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class ReplaceRefittedValues:
    """Mixin class to replace refitted values."""

    local_adata: ad.AnnData | None
    refit_adata: ad.AnnData | None

    def replace_refitted_values(
        self,
        train_data_nodes,
        aggregation_node,
        local_states,
        round_idx,
        clean_models,
    ):
        """Replace the values that were refitted in `local_adata`s.

        Parameters
        ----------
        train_data_nodes: list
            List of TrainDataNode.

        aggregation_node: AggregationNode
            The aggregation node.

        local_states: list[Dict]
            Local states. Required to propagate intermediate results.

        round_idx: int
            Index of the current round.

        clean_models: bool
            Whether to clean the models after the computation.

        Returns
        -------
        local_states: dict
            Local states, with refitted values

        round_idx: int
            The updated round index.
        """
        local_states, shared_states, round_idx = local_step(
            local_method=self.loc_replace_refitted_values,
            train_data_nodes=train_data_nodes,
            output_local_states=local_states,
            input_local_states=local_states,
            input_shared_state=None,
            aggregation_id=aggregation_node.organization_id,
            description="Replace refitted values in local adatas",
            round_idx=round_idx,
            clean_models=clean_models,
        )

        return local_states, round_idx

    @remote_data
    @log_remote_data
    @reconstruct_adatas
    def loc_replace_refitted_values(self, data_from_opener, shared_state):
        """
        Replace refitted values in local_adata from refit_adata.

        Parameters
        ----------
        data_from_opener : ad.AnnData
            AnnData returned by the opener. Not used.

        shared_state : dict
            Not used.
        """
        # Replace values in main object
        list_varm_keys = [
            "_normed_means",
            "LFC",
            "genewise_dispersions",
            "fitted_dispersions",
            "MAP_dispersions",
            "dispersions",
        ]
        for key in list_varm_keys:
            self.local_adata.varm[key][
                self.local_adata.varm["refitted"]
            ] = self.refit_adata.varm[key]

        # Take into account new all-zero genes
        new_all_zeroes_genes = self.local_adata.uns["new_all_zeroes_genes"]
        if len(new_all_zeroes_genes) > 0:
            self.local_adata.varm["_normed_means"][
                self.local_adata.var_names.get_indexer(new_all_zeroes_genes)
            ] = 0
            self.local_adata.varm["LFC"].loc[new_all_zeroes_genes, :] = 0

loc_replace_refitted_values(data_from_opener, shared_state)

Replace refitted values in local_adata from refit_adata.

Parameters:

Name Type Description Default
data_from_opener AnnData

AnnData returned by the opener. Not used.

 required
shared_state dict

Not used.

 required
Source code in fedpydeseq2/core/deseq2_core/replace_refitted_values/replace_refitted_values.py 
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@remote_data
@log_remote_data
@reconstruct_adatas
def loc_replace_refitted_values(self, data_from_opener, shared_state):
    """
    Replace refitted values in local_adata from refit_adata.

    Parameters
    ----------
    data_from_opener : ad.AnnData
        AnnData returned by the opener. Not used.

    shared_state : dict
        Not used.
    """
    # Replace values in main object
    list_varm_keys = [
        "_normed_means",
        "LFC",
        "genewise_dispersions",
        "fitted_dispersions",
        "MAP_dispersions",
        "dispersions",
    ]
    for key in list_varm_keys:
        self.local_adata.varm[key][
            self.local_adata.varm["refitted"]
        ] = self.refit_adata.varm[key]

    # Take into account new all-zero genes
    new_all_zeroes_genes = self.local_adata.uns["new_all_zeroes_genes"]
    if len(new_all_zeroes_genes) > 0:
        self.local_adata.varm["_normed_means"][
            self.local_adata.var_names.get_indexer(new_all_zeroes_genes)
        ] = 0
        self.local_adata.varm["LFC"].loc[new_all_zeroes_genes, :] = 0

replace_refitted_values(train_data_nodes, aggregation_node, local_states, round_idx, clean_models)

Replace the values that were refitted in local_adatas.

Parameters:

Name Type Description Default
train_data_nodes

List of TrainDataNode.

 required
aggregation_node

The aggregation node.

 required
local_states

Local states. Required to propagate intermediate results.

 required
round_idx

Index of the current round.

 required
clean_models

Whether to clean the models after the computation.

 required

Returns:

Name Type Description
local_states dict

Local states, with refitted values
round_idx int

The updated round index.
Source code in fedpydeseq2/core/deseq2_core/replace_refitted_values/replace_refitted_values.py 
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def replace_refitted_values(
    self,
    train_data_nodes,
    aggregation_node,
    local_states,
    round_idx,
    clean_models,
):
    """Replace the values that were refitted in `local_adata`s.

    Parameters
    ----------
    train_data_nodes: list
        List of TrainDataNode.

    aggregation_node: AggregationNode
        The aggregation node.

    local_states: list[Dict]
        Local states. Required to propagate intermediate results.

    round_idx: int
        Index of the current round.

    clean_models: bool
        Whether to clean the models after the computation.

    Returns
    -------
    local_states: dict
        Local states, with refitted values

    round_idx: int
        The updated round index.
    """
    local_states, shared_states, round_idx = local_step(
        local_method=self.loc_replace_refitted_values,
        train_data_nodes=train_data_nodes,
        output_local_states=local_states,
        input_local_states=local_states,
        input_shared_state=None,
        aggregation_id=aggregation_node.organization_id,
        description="Replace refitted values in local adatas",
        round_idx=round_idx,
        clean_models=clean_models,
    )

    return local_states, round_idx