bactoscoop.signalcorrelation
============================
.. py:module:: bactoscoop.signalcorrelation
Classes and public operations
-----------------------------
SignalCorrelation
~~~~~~~~~~~~~~~~~
.. py:class:: SignalCorrelation(df, channel1, channel2, feature, method_name, prepared_feature=None)
Select an implemented relationship between two channel-prefixed feature columns.
The feature must exist for both channels. calculate mutates the supplied DataFrame; prepared_feature can cache the numerical input arrays.
:param df: DataFrame to inspect, transform, or augment. Correlation mutates it in place and returns it.
:param channel1: First channel prefix for the matching feature.
:param channel2: Second channel prefix for the matching feature.
:param feature: Unprefixed shared feature name; corresponding channel-prefixed columns must exist.
:param method_name: Implemented correlation selector, such as pearson, manders, or ratio.
:param prepared_feature: Optional cached signal arrays and validity mask for a channel/feature pair.
:returns: None (no explicit return statement).
**Assigned state:** ``self.df``, ``self.channel1``, ``self.channel2``, ``self.feature``, ``self.method_name``, ``self.prepared_feature``, ``self.method``.
`View current source, line 16 <../source-code/signalcorrelation.html#signalcorrelation-16>`_.
SignalCorrelation.get_method
~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.get_method()
Get method.
**Return expressions in source:**
.. code-block:: python
methods[self.method_name]
**Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded.
`View current source, line 35 <../source-code/signalcorrelation.html#signalcorrelation-35>`_.
SignalCorrelation.validate_inputs
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.validate_inputs()
Validate inputs.
:returns: None (no explicit return statement).
**Explicitly raised exceptions:** ``ValueError``. Errors from called functions can also propagate or be recorded.
`View current source, line 60 <../source-code/signalcorrelation.html#signalcorrelation-60>`_.
SignalCorrelation.calculate
~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.calculate()
Calculate the selected signal relationship row by row.
Requires matching prefixed columns. Adds a function-name-suffixed column to df and returns that same DataFrame.
**Return expressions in source:**
.. code-block:: python
self.df
**Assigned state:** ``self.df``.
`View current source, line 71 <../source-code/signalcorrelation.html#signalcorrelation-71>`_.
SignalCorrelation.prepare_feature_pair
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.prepare_feature_pair(df, channel1, channel2, feature)
Prepare feature pair.
:param df: DataFrame to inspect, transform, or augment. Correlation mutates it in place and returns it.
:param channel1: First channel prefix for the matching feature.
:param channel2: Second channel prefix for the matching feature.
:param feature: Unprefixed shared feature name; corresponding channel-prefixed columns must exist.
**Return expressions in source:**
.. code-block:: python
{'signals1': signals1, 'signals2': signals2, 'valid_mask': valid_mask}
`View current source, line 101 <../source-code/signalcorrelation.html#signalcorrelation-101>`_.
SignalCorrelation.is_valid_signal
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.is_valid_signal(signal)
Is valid signal.
:param signal: Input ``signal`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
**Return expressions in source:**
.. code-block:: python
bool(signal_array.size and np.isfinite(signal_array).all())
False
`View current source, line 117 <../source-code/signalcorrelation.html#signalcorrelation-117>`_.
SignalCorrelation.ratio
~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.ratio(signal1, signal2)
Ratio.
:param signal1: Input ``signal1`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
:param signal2: Input ``signal2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
**Return expressions in source:**
.. code-block:: python
np.nan
signal1 / signal2
`View current source, line 125 <../source-code/signalcorrelation.html#signalcorrelation-125>`_.
SignalCorrelation.manders_overlap_coefficient
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.manders_overlap_coefficient(signal1, signal2)
Manders overlap coefficient.
:param signal1: Input ``signal1`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
:param signal2: Input ``signal2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
**Return expressions in source:**
.. code-block:: python
np.nan
np.sum(signal1 * signal2) / np.sqrt(np.sum(signal1 ** 2) * np.sum(signal2 ** 2))
`View current source, line 137 <../source-code/signalcorrelation.html#signalcorrelation-137>`_.
SignalCorrelation.pearson_correlation_coefficient
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.pearson_correlation_coefficient(signal1, signal2)
Pearson correlation coefficient.
:param signal1: Input ``signal1`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
:param signal2: Input ``signal2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
**Return expressions in source:**
.. code-block:: python
np.nan
stats.pearsonr(signal1, signal2)[0]
`View current source, line 150 <../source-code/signalcorrelation.html#signalcorrelation-150>`_.
SignalCorrelation.li_icq
~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.li_icq(signal1, signal2)
Li icq.
:param signal1: Input ``signal1`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
:param signal2: Input ``signal2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
**Return expressions in source:**
.. code-block:: python
np.nan
(np.sum(product) / len(signal1) - 0.5) * 2
`View current source, line 159 <../source-code/signalcorrelation.html#signalcorrelation-159>`_.
SignalCorrelation.spearman_rank_correlation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.spearman_rank_correlation(signal1, signal2)
Spearman rank correlation.
:param signal1: Input ``signal1`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
:param signal2: Input ``signal2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
**Return expressions in source:**
.. code-block:: python
np.nan
stats.spearmanr(signal1, signal2)[0]
`View current source, line 172 <../source-code/signalcorrelation.html#signalcorrelation-172>`_.
SignalCorrelation.kendall_tau
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.kendall_tau(signal1, signal2)
Kendall tau.
:param signal1: Input ``signal1`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
:param signal2: Input ``signal2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
**Return expressions in source:**
.. code-block:: python
np.nan
corr
`View current source, line 181 <../source-code/signalcorrelation.html#signalcorrelation-181>`_.
SignalCorrelation.distance_correlation
~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~
.. py:method:: SignalCorrelation.distance_correlation(signal1, signal2)
Biased sample distance correlation; undefined profiles return NaN.
:param signal1: Input ``signal1`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
:param signal2: Input ``signal2`` consumed by this implementation; its exact use is visible in the linked source below. No maintained parameter description is present in the original docstring.
**Return expressions in source:**
.. code-block:: python
np.nan
float(np.sqrt(np.clip(correlation_squared, 0, 1)))
`View current source, line 191 <../source-code/signalcorrelation.html#signalcorrelation-191>`_.
.. raw:: html
Original docstring (legacy wording may differ from the current signature)
.. code-block:: text
Biased sample distance correlation; undefined profiles return NaN.
.. raw:: html
Original docstring (legacy wording may differ from the current signature)
.. code-block:: text
Intersect probability histograms using shared bins for both profiles.
.. raw:: html