Results for making a one-base change from the reference base to Selene_ get_score_matrix_for ( feature, reference_mask=None, dtype= ) ¶Įxtracts a feature from the in silico mutagenesis resultsĪs a matrix, where the reference base positions hold the valueįor the reference prediction, and alternative positions hold the The in silico mutagenesis results that were stored in the Input_path ( str) – A path to the file of comma separated input values. Stored in a file of comma separated values (CSV). Static from_file ( input_path, sequence_type= ) ¶
ValueError – If the input data frame contains a base not included in theĮxception – If multiple reference positions are specified in the inputĮxception – If the input data does not contain scores for every mutation That the in silico mutagenesis results are associated Sequence_type ( class, optional) – Default is selene_. ISMResult ( data_frame, sequence_type= ) ¶Īn object storing the results of an in silico mutagenesisĭata_frame ( pandas.DataFrame) – The data frame with the results from the in silico **kwargs ( dict) – Keyword arguments to pass to seaborn.heatmap. The in silico mutagenesis results are associated with. Is the length of the sequence, and \(N\) is the size of theĪlphabet) containing True at positions in the heatmap to Mask ( numpy.ndarray, dtype=bool or None, optional) – Default is None. The sequence, and \(N\) is the size of the alphabet)Ĭontaining the scores for each base change at each position. Score_matrix ( numpy.ndarray) – An \(L \times N\) array (where \(L\) is the length of In silico mutagenesis experiment, on a heatmap. Plots the input matrix of scores, generally those produced by an heatmap ( score_matrix, mask=None, sequence_type=, **kwargs ) ¶ We have included an example of the output from a sequence_logo ValueError – If the number of colors in color_palette does not match the Number of characters in the alphabet of sequence_type.
ValueError – If the number of columns in score_matrix does not match the The axes containing the sequence logo plot. With lor_palette, and will have as manyĬolors as there are characters in the input sequence alphabet. If left as None, a default palette will be made A list containing the hex codes or names ofĬolors to use, appearing in the order of the bases of the Than None, then no such guarantee can be made.Ĭolor_scheme ( list(str) or None, optional) – Default is None. The tops and bottoms of characters at each position in the The actual values, and that there are no extra gaps between Is preferred, as it ensures all character heights correspond to Object that specifies the properties of the font to use for Should generally be a subclass of selene_.įont_properties ( matplotlib.font_manager.FontProperties or None, optional) – Default is None.
A value of 0 will not draw anyĪx ( or None, optional) – Default is None. The width of each character in the plotted logo.Ī value of 1 will mean that there is no gap between each theĬharacters at each position. ‘value’ - Bases go in the order of their value, with the largest at the bottom. ‘alpha’ - Bases go in the order they are found in the sequence alphabet.
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