geom_alignedSeq

A class that represents the sequence alignment diagram

Sample code

from plotnine import ggplot, coord_fixed
from plotnineseqsuite import geom_alignedSeq, theme_seq
from plotnineseqsuite.data import seqs_dna
ggplot() + geom_alignedSeq(seqs_dna['MA0013.1']) + theme_seq() + coord_fixed()

Init param

geom_alignedSeq(self,
             data: list[str] | dict | None = None,
             seq_names: list[str] | None = None,
             seq_type: str = 'AUTO',
             namespace: list[str] | None = None,
             font: str = 'roboto_medium',
             stack_width: float = 0.75,
             border_col: str = 'grey',
             scheme_applied: str = 'BACKGROUND',
             no_scheme_col: str = '#000000',
             col_scheme: Dict | str = 'AUTO',
             low_col: str = 'black',
             high_col: str = 'yellow',
             na_col: str = '#333333',
             **kwargs: Any) -> Any

• data
  Sequence data or corresponding dict.
• seq_names
  The name corresponding to the sequence data.
• seq_type
  OTHER, AA, DNA, RNA
• namespace
  The letter corresponding to the data.
• font
  Font value
• stack_width
  The ratio of the size of letters to the standard unit width.
• border_col The color of the border in the background. When it is None, the border of the background will disappear.
• scheme_applied BACKGROUND or LETTER. Indicates the target to which the color scheme applies.
• no_scheme_col
  When a color scheme is applied to the background, this indicates the color of the letters. When a color scheme is applied to letters, this indicates the color of the background.
• col_scheme
  Color scheme.
• low_col
  Continuous color schemes are available.
• high_col
  Continuous color schemes are available.
• na_col
  It is available when the corresponding namespace do not have a color matching value defined.
• kwargs
  Other arguments passed on to layer().

properties

• bg_data
  DataFrame.
• letter_data
  DataFrame.
• scale_x_continuous
  A custom scale_x_continuous.
• scale_y_continuous
  A custom scale_y_continuous.
• xlab
  A custom xlab.
• ylab
  A custom ylab.
• colscale_opts
  A custom scale_fill_gradient or custom scale_fill_manual.