Logo Data, Options, and Format

class weblogo.logo.LogoData(length: Optional[int] = None, alphabet: Optional[weblogo.seq.Alphabet] = None, counts: Optional[numpy.ndarray] = None, entropy: Optional[numpy.ndarray] = None, entropy_interval: Optional[numpy.ndarray] = None, weight: Optional[numpy.ndarray] = None)

The data needed to generate a sequence logo.

Parameters:

• alphabet – The set of symbols to count. See also –sequence-type, –ignore-lower-case
• length – All sequences must be the same length, else WebLogo will return an error
• counts – An array of character counts
• entropy – The relative entropy of each column
• entropy_interval – entropy confidence interval

csv() → str

Return logodata as a csv formatted string

classmethod from_counts(alphabet: Optional[weblogo.seq.Alphabet], counts: numpy.ndarray, prior: Optional[numpy.ndarray] = None) → weblogo.logo.LogoData

Build a LogoData object from counts.

classmethod from_seqs(seqs: weblogo.seq.SeqList, prior: Optional[numpy.ndarray] = None) → weblogo.logo.LogoData

Build a LogoData object from a SeqList, a list of sequences.

class weblogo.logo.LogoFormat(logodata: weblogo.logo.LogoData, logooptions: Optional[weblogo.logo.LogoOptions] = None)

Specifies the format of the logo. Requires LogoData and LogoOptions objects.

>>> logodata = LogoData.from_seqs(seqs)
>>> logooptions = LogoOptions()

>>> logooptions.title = "A Logo Title"
>>> format = LogoFormat(logodata, logooptions)

Raises:ArgumentError – if arguments are invalid.

class weblogo.logo.LogoOptions(**kwargs)

A container for all logo formatting options. Not all of these are directly accessible through the CLI or web interfaces.

To display LogoOption defaults:

>>> from weblogo import *
>>> LogoOptions()

All physical lengths are measured in points. (72 points per inch, 28.3 points per cm)

Parameters:

• creator_text – Embedded as comment in figures.
• logo_title – Creates title for the sequence logo
• logo_label – An optional figure label, added to the top left (e.g. ‘(a)’).
• unit_name – See std_units for options. (Default ‘bits’)
• yaxis_label – Defaults to unit_name
• xaxis_label – Add a label to the x-axis, or hide x-axis altogether.
• fineprint – Defaults to WebLogo name and version
• show_yaxis – Display entropy scale along y-axis (default: True)
• show_xaxis – Display sequence numbers along x-axis (default: True)
• show_ends – Display label at the ends of the sequence (default: False)
• show_fineprint – Toggle display of the WebLogo version information in the lower right corner. Optional, but we appreciate the acknowledgment.
• show_errorbars – Draw errorbars (default: False)
• show_boxes – Draw boxes around stack characters (default: True)
• debug – Draw extra graphics debugging information.
• rotate_numbers – Draw xaxis numbers with vertical orientation?
• scale_width – boolean, scale width of characters proportional to ungaps
• pad_right – Make a single line logo the same width as multiline logos (default: False)
• stacks_per_line – Maximum number of logo stacks per logo line. (Default: 40)
• yaxis_tic_interval – Distance between ticmarks on y-axis(default: 1.0)
• yaxis_minor_tic_ratio – Distance between minor tic ratio
• yaxis_scale – Sets height of the y-axis in designated units
• xaxis_tic_interval – Distance between ticmarks on x-axis(default: 1.0)
• number_interval – Distance between ticmarks (default: 1.0)
• shrink_fraction – Proportional shrinkage of characters if show_boxes is true.
• errorbar_fraction – Sets error bars display proportion
• errorbar_width_fraction – Sets error bars display
• errorbar_gray – Sets error bars’ gray scale percentage (default .75)
• resolution – Dots per inch (default: 96). Used for bitmapped output formats
• default_color – Symbol color if not otherwise specified
• color_scheme – A custom color scheme can be specified using CSS2 (Cascading Style Sheet) syntax. E.g. ‘red’, ‘#F00’, ‘#FF0000’, ‘rgb(255, 0, 0)’, ‘rgb(100%, 0%, 0%)’ or ‘hsl(0, 100%, 50%)’ for the color red.
• stack_width – Scale the visible stack width by the fraction of symbols in the column (I.e. columns with many gaps of unknowns are narrow.) (Default: yes)
• stack_aspect_ratio – Ratio of stack height to width (default: 5)
• logo_margin – Default: 2 pts
• stroke_width – Default: 0.5 pts
• tic_length – Default: 5 pts
• stack_margin – Default: 0.5 pts
• small_fontsize – Small text font size in points
• fontsize – Regular text font size in points
• title_fontsize – Title text font size in points
• number_fontsize – Font size for axis-numbers, in points.
• text_font – Select font for labels
• logo_font – Select font for Logo
• title_font – Select font for Logo’s title
• first_index – Index of first position in sequence data
• logo_start – Lower bound of sequence to display
• logo_end – Upper bound of sequence to display

weblogo.logo.parse_prior(composition: Any, alphabet: weblogo.seq.Alphabet, weight: Optional[float] = None) → Optional[numpy.ndarray]

Parse a description of the expected monomer distribution of a sequence.

Valid compositions:

• None or ‘none’

  No composition specified

• ‘auto’ or ‘automatic’

  Use the typical average distribution for proteins and an equiprobable distribution for everything else.

• ‘equiprobable’

  All monomers have the same probability.

• a percentage, e.g. ‘45%’ or a fraction ‘0.45’

  The fraction of CG bases for nucleotide alphabets

• a species name, e.g. ‘E. coli’, ‘H. sapiens’,

  Use the average CG percentage for the species’s genome.

• An explicit distribution

  e.g. {‘A’:10, ‘C’:40, ‘G’:40, ‘T’:10}

returns a dict of {monomer: probability} pairs.

weblogo.logo.read_seq_data(fin: Union[_io.StringIO, _io.TextIOWrapper, None], input_parser: Callable = <function read>, alphabet: Optional[weblogo.seq.Alphabet] = None, ignore_lower_case: bool = False, max_file_size: int = 0) → weblogo.seq.SeqList

Read sequence data from the input stream and return a seqs object.

The environment variable WEBLOGO_MAX_FILE_SIZE overides the max_file_size argument. Used to limit the load on the WebLogo webserver.