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Fix docs to remove reference to default behaviour including soma_join…
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…id (#1292)
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ivirshup authored Oct 1, 2024
1 parent 56ab5b0 commit b09d336
Showing 1 changed file with 5 additions and 9 deletions.
Original file line number Diff line number Diff line change
Expand Up @@ -430,11 +430,9 @@ class ExperimentDataPipe(pipes.IterDataPipe[Dataset[ObsAndXDatum]]): # type: ig
The ``return_sparse_X`` parameter controls whether the ``X`` data is returned as a dense or sparse
:class:`torch.Tensor`. If the model supports use of sparse :class:`torch.Tensor`\ s, this will reduce memory usage.
The ``obs_column_names`` parameter determines the data columns that are returned in the ``obs`` Tensor. The first
element is always the ``soma_joinid`` of the ``obs`` :class:`pandas.DataFrame` (or, equivalently, the
``soma_dim_0`` of the ``X`` matrix). The remaining elements are the ``obs`` columns specified by
``obs_column_names``, and string-typed columns are encoded as integer values. If needed, these values can be decoded
by obtaining the encoder for a given ``obs`` column name and calling its ``inverse_transform`` method:
The ``obs_column_names`` parameter determines the data columns that are returned in the ``obs`` Tensor. String-typed
columns are encoded as integer values. If needed, these values can be decoded by obtaining the encoder for a given
``obs`` column name and calling its ``inverse_transform`` method:
>>> exp_data_pipe.obs_encoders["<obs_attr_name>"].inverse_transform(encoded_values)
Expand Down Expand Up @@ -489,10 +487,8 @@ def __init__(
The query used to filter along the ``var`` axis. If not specified, all ``var`` columns (genes/features)
will be returned.
obs_column_names:
The names of the ``obs`` columns to return. The ``soma_joinid`` index "column" does not need to be
specified and will always be returned. If not specified, only the ``soma_joinid`` will be returned.
If custom encoders are passed, this parameter must not be used, since the columns will be inferred
automatically from the encoders.
The names of the ``obs`` columns to return. If custom encoders are passed, this parameter must not be used,
since the columns will be inferred automatically from the encoders.
batch_size:
The number of rows of ``obs`` and ``X`` data to return in each iteration. Defaults to ``1``. A value of
``1`` will result in :class:`torch.Tensor` of rank 1 being returns (a single row); larger values will
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