geom_logo

A class that represents the sequence logo

Sample code

from plotnine import ggplot
from plotnineseqsuite import geom_logo, theme_seq
from plotnineseqsuite.data import seqs_dna
ggplot() + geom_logo(seqs_dna['MA0001.1']) + theme_seq()

Init param

geom_logo(self,
             data: list[str] | ndarray | dict | None = None,
             method: str = 'bits',
             seq_type: str = 'AUTO',
             namespace: list[str] | None = None,
             font: str = 'roboto_medium',
             stack_width: float = 0.95,
             rev_stack_order: bool = False,
             col_scheme: Dict | str = 'AUTO',
             low_col: str = 'black',
             high_col: str = 'yellow',
             na_col: str = '#333333',
             **kwargs: Any) -> Any

• data
  Sequence data or PFM or corresponding dict.
• method
  bits, probability, custom
• seq_type
  OTHER, AA, DNA, RNA
• namespace
  The letter corresponding to the data. If the type of data is ndarray, the order of the namespaces must correspond to that of ndarray.
• font
  Font value
• stack_width
  The ratio of the size of letters to the standard unit width.
• rev_stack_order
  Order of letter stack is reversed.
• col_scheme
  Color scheme of the letters.
• low_col
  Continuous color schemes are available.
• high_col
  Continuous color schemes are available.
• na_col
  Used when the letters in the corresponding namespace do not have a color matching value defined.
• kwargs
  Other arguments passed on to layer().

properties

• data
  DataFrame.
• scale_x_continuous
  A custom scale_x_continuous.
• xlab
  A custom xlab.
• ylab
  A custom ylab.
• colscale_opts
  A custom scale_fill_gradient or custom scale_fill_manual.y