:py:mod:`squid.impress`
=======================

.. py:module:: squid.impress


Module Contents
---------------

Classes
~~~~~~~

.. autoapisummary::

   squid.impress.hidden_prints



Functions
~~~~~~~~~

.. autoapisummary::

   squid.impress.plot_y_hist
   squid.impress.plot_performance
   squid.impress.plot_additive_logo
   squid.impress.plot_pairwise_matrix
   squid.impress.plot_y_vs_yhat
   squid.impress.plot_y_vs_phi
   squid.impress.plot_eig_vals
   squid.impress.plot_eig_vecs



.. py:function:: plot_y_hist(y_mut, save_dir=None)

   
   Function for visualizing histogram of inferred predictions for MAVE dataset.

   :param y_mut: Inferred predictions for sequences (shape: (N,1)).
   :type y_mut: numpy.ndarray
   :param save_dir: Directory for saving figures to file.
   :type save_dir: str

   :rtype: matplotlib.pyplot.Figure















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.. py:function:: plot_performance(model, info, save_dir=None)

   
   Function for visualizing MAVE-NN model training performance.

   :param model: MAVE-NN model object.
   :type model: mavenn.src.model.Model
   :param info: MAVE-NN estimated variational information (I_pred), in bits.
   :type info: float
   :param save_dir: Directory for saving figures to file.
   :type save_dir: str

   :rtype: matplotlib.pyplot.Figure















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.. py:function:: plot_additive_logo(logo, center=True, view_window=None, alphabet=['A', 'C', 'G', 'T'], fig_size=None, save_dir=None, save_name=None)

   
   Function for visualizing MAVE-NN additive model parameters.

   :param logo: Additive model parameters (shape: (L,C)).
   :type logo: numpy.ndarray
   :param center: If True, the stack of characters at each position will be centered
                  around zero. This is accomplished by subtracting the mean value in
                  each row of the matrix from each element in that row.
   :type center: bool
   :param view_window: Index of start and stop position along sequence to probe;
                       i.e., [start, stop], where start < stop and both entries
                       satisfy 0 <= int <= L.
   :type view_window: [int, int]
   :param alphabet: The alphabet used to determine the C characters in the logo such that
                    each entry is a string; e.g., ['A','C','G','T'] for DNA.
   :type alphabet: list
   :param fig_size: Width, height in inches for matplotlib.pyplot figure.
   :type fig_size: [float, float]
   :param save_dir: Directory for saving figure to file.
   :type save_dir: str
   :param save_name: If save_dir is not None, save_name sets the filename for saving figure to file.
   :type save_name: str

   :rtype: matplotlib.pyplot.Figure















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.. py:function:: plot_pairwise_matrix(theta_lclc, view_window=None, alphabet=['A', 'C', 'G', 'T'], threshold=None, save_dir=None)

   
   Function for visualizing MAVE-NN pairwise model parameters.

   :param theta_lclc: Pairwise model parameters (shape: (L,C,L,C)).
   :type theta_lclc: numpy.ndarray
   :param view_window: Index of start and stop position along sequence to probe;
                       i.e., [start, stop], where start < stop and both entries
                       satisfy 0 <= int <= L.
   :type view_window: [int, int]
   :param alphabet: The alphabet used to determine the C characters in the logo such that
                    each entry is a string; e.g., ['A','C','G','T'] for DNA.
   :type alphabet: list
   :param threshold: Define threshold window centered around zero for removing potential noise
                     from parameters for cleaner pairwise matrix visualization
   :type threshold: float
   :param save_dir: Directory for saving figures to file.
   :type save_dir: str

   :rtype: matplotlib.pyplot.Figure















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.. py:function:: plot_y_vs_yhat(model, mave_df, save_dir=None)

   
   Function for visualizing comparison of MAVE values and MAVE-NN predictions.

   :param model: MAVE-NN model object.
   :type model: mavenn.src.model.Model
   :param mave_df: Dataframe containing MAVE training splits, y floats, and x strings  (shape : (N,3))
   :type mave_df: pandas.core.frame.DataFrame
   :param save_dir: Directory for saving figures to file.
   :type save_dir: str

   :rtype: matplotlib.pyplot.Figure















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.. py:function:: plot_y_vs_phi(model, mave_df, save_dir=None)

   
   Function for visualizing comparison of MAVE values and MAVE-NN latent phenotypes.

   :param model: MAVE-NN model object.
   :type model: mavenn.src.model.Model
   :param mave_df: Dataframe containing MAVE training splits, y floats, and x strings  (shape : (N,3))
   :type mave_df: pandas.core.frame.DataFrame
   :param save_dir: Directory for saving figures to file.
   :type save_dir: str

   :rtype: matplotlib.pyplot.Figure















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.. py:function:: plot_eig_vals(vals, save_dir=None)

   
   Function for visualizing eigenvalue spectrum, if using PCA.

   :param vals: Eigenvalues obtained from PCA.
   :type vals: numpy.ndarray
   :param save_dir: Directory for saving figures to file.
   :type save_dir: str

   :rtype: matplotlib.pyplot.Figure















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.. py:function:: plot_eig_vecs(U, v1, v2, save_dir=None)

   
   Function for visualizing subspace defined by two eigenvectors, if using PCA.

   :param U: Eigenvectors obtained from PCA.
   :type U: numpy.ndarray
   :param v1: Index of first eigenvector.
   :type v1: int
   :param v2: Index of second eigenvector.
   :type v2: int
   :param save_dir: Directory for saving figures to file.
   :type save_dir: str

   :rtype: matplotlib.pyplot.Figure















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.. py:class:: hidden_prints


   
   Function to temporarily hide print statements.
















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   .. py:method:: __enter__()


   .. py:method:: __exit__(exc_type, exc_val, exc_tb)