diff --git a/src/sceptr/__init__.py b/src/sceptr/__init__.py index dd81f2b..1453ac0 100644 --- a/src/sceptr/__init__.py +++ b/src/sceptr/__init__.py @@ -20,9 +20,12 @@ def calc_cdist_matrix(anchors: DataFrame, comparisons: DataFrame) -> ndarray: Parameters ---------- anchors : DataFrame - DataFrame in the :ref:`prescribed format `. + DataFrame specifying the first (anchor) collection of input TCRs. + It must be in the :ref:`prescribed format `. + comparisons : DataFrame - DataFrame in the :ref:`prescribed format `. + DataFrame specifying the second (comparison) collection of input TCRs. + It must be in the :ref:`prescribed format `. Returns ------- @@ -40,7 +43,8 @@ def calc_pdist_vector(instances: DataFrame) -> ndarray: Parameters ---------- instances : DataFrame - DataFrame in the :ref:`prescribed format `. + DataFrame specifying the input TCRs. + It must be in the :ref:`prescribed format `. Returns ------- @@ -58,7 +62,8 @@ def calc_vector_representations(instances: DataFrame) -> ndarray: Parameters ---------- instances : DataFrame - DataFrame in the :ref:`prescribed format `. + DataFrame specifying the input TCRs. + It must be in the :ref:`prescribed format `. Returns ------- @@ -77,11 +82,13 @@ def calc_residue_representations(instances: DataFrame) -> ResidueRepresentations Parameters ---------- instances : DataFrame - DataFrame in the :ref:`prescribed format `. + DataFrame specifying the input TCRs. + It must be in the :ref:`prescribed format `. Returns ------- :py:class:`~sceptr.model.ResidueRepresentations` + An array of representation vectors for each amino acid residue in the tokenised forms of the input TCRs. For details on how to interpret/use this output, please refer to the documentation for :py:class:`~sceptr.model.ResidueRepresentations`. """ return get_default_model().calc_residue_representations(instances) diff --git a/src/sceptr/model.py b/src/sceptr/model.py index 8c25986..c3e9c05 100644 --- a/src/sceptr/model.py +++ b/src/sceptr/model.py @@ -137,7 +137,8 @@ def calc_vector_representations(self, instances: DataFrame) -> ndarray: Parameters ---------- instances : DataFrame - DataFrame in the :ref:`prescribed format `. + DataFrame specifying the input TCRs. + It must be in the :ref:`prescribed format `. Returns ------- @@ -160,11 +161,13 @@ def calc_residue_representations(self, instances: DataFrame) -> ResidueRepresent Parameters ---------- instances : DataFrame - DataFrame in the :ref:`prescribed format `. + DataFrame specifying the input TCRs. + It must be in the :ref:`prescribed format `. Returns ------- :py:class:`~sceptr.model.ResidueRepresentations` + An array of representation vectors for each amino acid residue in the tokenised forms of the input TCRs. For details on how to interpret/use this output, please refer to the documentation for :py:class:`~sceptr.model.ResidueRepresentations`. """ if not isinstance(self._tokeniser, CdrTokeniser): @@ -239,9 +242,12 @@ def calc_cdist_matrix(self, anchors: DataFrame, comparisons: DataFrame) -> ndarr Parameters ---------- anchors : DataFrame - DataFrame in the :ref:`prescribed format `. + DataFrame specifying the first (anchor) collection of input TCRs. + It must be in the :ref:`prescribed format `. + comparisons : DataFrame - DataFrame in the :ref:`prescribed format `. + DataFrame specifying the second (comparison) collection of input TCRs. + It must be in the :ref:`prescribed format `. Returns ------- @@ -263,7 +269,8 @@ def calc_pdist_vector(self, instances: DataFrame) -> ndarray: Parameters ---------- instances : DataFrame - DataFrame in the :ref:`prescribed format `. + DataFrame specifying the input TCRs. + It must be in the :ref:`prescribed format `. Returns -------