digitaldna.SequencePlots

class digitaldna.SequencePlots(alphabet=None)[source]

The Digital DNA plots utility class.

Parameters:
alphabet : string, optional

The sequences’ alphabet, used to show prettier labels, possible values are:

  • ‘b3_type’
  • ‘b3_content’
  • ‘b6_content’
  • None

Default: None

Methods

plot_alphabet_distribution(X) This function produces a box plot where each box represents the distribution of a letter in the sequences.
plot_intersequence_entropy(X) This function produces a composite plot.
plot_intrasequence_entropy(X) This function produces a box plot with a single box representing the distribution of the intra-sequence entropies (the Shannon Entropy computed over a single digital dna sequence).
plot_sequences_color(X) This function produces a matrix image where each row is a digital dna sequence and each letter is represented by a different color.
__init__(alphabet=None)[source]

Initialize self. See help(type(self)) for accurate signature.

plot_alphabet_distribution(X)[source]

This function produces a box plot where each box represents the distribution of a letter in the sequences. The alphabet is inferred from the sequences.

Parameters:
X : array-like, shape (n_samples, 1), mandatory

The input sequences of digital dna
Returns:
y : an instance of self
plot_intersequence_entropy(X)[source]

This function produces a composite plot. On the left a boxplot representing the distribution of the inter-sequence entropy (Shannon’s Entropy of the letters in the same with same sequence index but in different sequences). On the right a scatterplot of the entropies ordered by sequence index.

Parameters:
X : array-like, shape (n_samples, 1), mandatory

The input sequences of digital dna
Returns:
y : an instance of self
plot_intrasequence_entropy(X)[source]

This function produces a box plot with a single box representing the distribution of the intra-sequence entropies (the Shannon Entropy computed over a single digital dna sequence).

Parameters:
X : array-like, shape (n_samples, 1), mandatory

The input sequences of digital dna
Returns:
y : an instance of self
plot_sequences_color(X)[source]

This function produces a matrix image where each row is a digital dna sequence and each letter is represented by a different color.

Parameters:
X : array-like, shape (n_samples, 1), mandatory

The input sequences of digital dna
Returns:
y : an instance of self