buscoplotpy.graphics package

Submodules

buscoplotpy.graphics.chromoplot module

buscoplotpy.graphics.chromosome module

class buscoplotpy.graphics.chromosome.Chromosome(name: str, x_start: float, x_end: float, y_start: float, y_end: float, size: float, horizontal: bool = True, round_edges: bool = False, color: str = '', genes_dataframe: DataFrame = None)

Bases: object

add_gene_density(genes_dataframe: DataFrame) → None

Adds gene density to the Chromosome.

Parameters:

• genes_dataframe (pd.DataFrame): The dataframe containing the gene density information.

add_label(x: float, y: float, text: str, rotation: float = 0, ha: str = 'left', va: str = 'baseline')

Add a label to the plot at the specified coordinates.

Parameters:

• x (float): The x-coordinate of the label.

• y (float): The y-coordinate of the label.

• text (str): The text of the label.

• ha (str, optional): The horizontal alignment of the label. Defaults to ‘left’.

• va (str, optional): The vertical alignment of the label. Defaults to ‘baseline’.

add_region(anchor_point: (<class 'float'>, <class 'float'>), width: float, height: float, color: str = 'black', linewidth: int = 1)

Adds a region to the list of regions.

Parameters:

• anchor_point (Tuple[float, float]): The anchor point of the region.

• width (float): The width of the region.

• height (float): The height of the region.

• color (str, optional): The color of the region. Defaults to ‘black’.

• linewidth (int, optional): The linewidth of the region. Defaults to 1.

get_relative_position(position: int) -> (<class 'float'>, <class 'float'>)

Returns the position relative to the start and end of the chromosome.

Parameters:

• position (int): The position to convert.

Returns:

• float: The position relative to the start and end of the chromosome.

plot(fig, ax)

Plot the chromosome on the given axes.

Parameters:

• ax: The axes to plot on.

• round_edges: A boolean indicating whether to round the edges of the chromosome.

Returns:

None

buscoplotpy.graphics.karyoplot module

buscoplotpy.graphics.karyoplot.karyoplot(karyotype: DataFrame, output_file: str = '', title: str = 'Karyoplot', fulltable: DataFrame = None, selected_sequences: list = [], dpi: int = 300, chrs_limit: int = 30, plt_show: bool = False, palette: False = 'green', bbox_inches: str = 'tight', dim: int = 2) → None

Plot a karyotype based on the karyotype file and the BUSCO fulltable.

Parameters:

• karyotype (pd.DataFrame): The karyotype DataFrame.

• output_file (str, optional): The path to save the output plot.

• title (str, optional): The title of the plot.

• fulltable (pd.DataFrame): The BUSCO’s full table DataFrame.

• dpi (int, optional): The DPI (dots per inch) of the output plot. Default is 300.

• chrs_limit (int, optional): The maximum number of chromosomes to plot. Default is 30.

• plt_show (bool, optional): Whether to show the plot. Default is False.

• palette (str, optional): The color palette to use. Default is ‘green’.

• bbox_inches (str, optional): The bbox_inches parameter of the plt.savefig() function. Default is ‘tight’.

• dim (int, optional): The dimension of the chromosomes. Defaults to 2.

Output:

• The karyotype plot in png format.

Returns:

• None

buscoplotpy.graphics.label module

class buscoplotpy.graphics.label.Label(x: float, y: float, text: str, rotation: float = 0, ha: str = 'left', va: str = 'baseline')

Bases: object

plot(ax)

Plot the text on the given axes.

Parameters:

ax (matplotlib.axes.Axes): The axes on which to plot the text.

buscoplotpy.graphics.link module

class buscoplotpy.graphics.link.Link(C1: Chromosome, C2: Chromosome, p_1: int, p_2: int, color: str = '#d1d1d1', straight_line: bool = False, horizontal: bool = False)

Bases: object

bezier_curve(t, p0, p1, p2, p3)

Calculate the Bezier curve at time t.

Parameters:

• t (float): The time parameter between 0 and 1.

• p0 (float): The starting point of the curve.

• p1 (float): The first control point.

• p2 (float): The second control point.

• p3 (float): The ending point of the curve.

Returns:

• float: The position on the Bezier curve at time t.

plot(ax)

Plot the link on the given axes.

Parameters:

• ax (matplotlib.axes.Axes): The axes on which to plot the link.

buscoplotpy.graphics.organism_busco_barplot module

buscoplotpy.graphics.organism_busco_barplot.organism_busco_barplot(df: DataFrame, group_name: str = '', organism_name: str = '', out_path: str = './', filename: str = 'busco_barplot', dpi: int = 300, plt_show: bool = False) → None

Generate a barplot to visualize the completeness of assembly for different organisms on the same BUSCO dataset.

Parameters:

• df (pd.DataFrame): The input dataframe containing the data to be plotted.

• group_name (str): The name of the group to be plotted.

• organism_name (str): The name of the organism to be plotted.

• out_path (str): The path where the plot image will be saved.

• filename (str): The name of the plot image file.

Output:

• A barplot image with the completeness of assembly for different organisms on the same BUSCO dataset in .png format.

Returns:

• None

buscoplotpy.graphics.synteny module

buscoplotpy.graphics.synteny.generate_bottom_karyotype(karyotype: DataFrame, dim: int, round_edges: bool) → dict

Generate a bottom karyotype plot.

Parameters:

• karyotype (pd.DataFrame): DataFrame containing karyotype information.

• dim (int): Dimension of the karyotype plot.

• round_edges (bool): Whether to round the edges of the chromosomes.

Returns:

• dict: Dictionary containing the generated chromosomes.

buscoplotpy.graphics.synteny.generate_left_karyotype(karyotype: DataFrame, dim: int, round_edges: bool) → dict

Plot the left karyotype chromosomes.

Parameters:

• karyotype: pandas DataFrame containing information about the chromosomes

• dim: dimension of the chromosomes

• round_edges: flag indicating whether to round the edges of the chromosomes

Returns:

• C: A dictionary mapping chromosome names to their corresponding Chromosome objects.

buscoplotpy.graphics.synteny.generate_links(ft_1: DataFrame, ft_2: DataFrame, right_chromosomes: dict, left_chromosomes: dict, link_colors: str, straight_line: bool, horizontal: bool) → list

Generates and plots links between two data frames.

Parameters:

• ft_1 (pd.DataFrame): First full table data frame.

• ft_2 (pd.DataFrame): Second full table data frame.

• right_chromosomes (dict): Dictionary mapping sequence names to right chromosomes.

• left_chromosomes (dict): Dictionary mapping sequence names to left chromosomes.

• link_colors (str): Dictionary mapping sequence names to link colors.

• straight_line (bool): Flag indicating whether to plot links as straight lines.

Returns:

• None

buscoplotpy.graphics.synteny.generate_right_karyotype(karyotype: DataFrame, dim: int, round_edges: bool) → dict

Plot the left karyotype chromosomes.

Parameters:

• karyotype: pandas DataFrame containing information about the chromosomes

• dim: dimension of the chromosomes

• round_edges: flag indicating whether to round the edges of the chromosomes

Returns:

• C: A dictionary mapping chromosome names to their corresponding Chromosome objects.

buscoplotpy.graphics.synteny.generate_up_karyotype(karyotype: DataFrame, dim: int, round_edges: bool) → dict

Generate an upward karyotype plot based on the given karyotype data.

Parameters:

• karyotype (pd.DataFrame): DataFrame containing karyotype information.

• dim (int): Dimension of the karyotype plot.

• round_edges (bool): Flag indicating whether to use rounded edges for the chromosomes.

Returns:

• dict: Dictionary containing the generated karyotype plot.

buscoplotpy.graphics.synteny.horizontal_synteny_plot(ft_1: ~pandas.core.frame.DataFrame, ft_2: ~pandas.core.frame.DataFrame, karyotype_1: ~pandas.core.frame.DataFrame, karyotype_2: ~pandas.core.frame.DataFrame, title: str = 'Synteny plot', dim: int = 2, figsize: (<class 'int'>, <class 'int'>) = (30, 10), dpi: int = 300, round_edges: bool = False, link_colors: dict = {}, straight_line: bool = False, output_path: str = None, bbox_inches: str = 'tight', plt_show: bool = False)

Generate a horizontal synteny plot.

Parameters:

• ft_1 (pd.DataFrame): Full table for the left karyotype.

• ft_2 (pd.DataFrame): Full table for the right karyotype.

• karyotype_1 (pd.DataFrame): Karyotype dataframe for the left karyotype.

• karyotype_2 (pd.DataFrame): Karyotype dataframe for the right karyotype.

• title (str, optional): The title of the plot. Defaults to ‘Synteny plot’.

• dim (int, optional): The dimension of the chromosomes. Defaults to 2.

• figsize (tuple, optional): The size of the plot figure. Defaults to (18, 10).

• dpi (int, optional): The resolution of the plot figure. Defaults to 300.

• round_edges (bool, optional): Whether to round the edges of the karyotype blocks. Defaults to False.

• link_colors (dict, optional): A dictionary mapping link colors to chromosome pairs. Defaults to {}.

• straight_line (bool, optional): Whether to use straight lines for links. Defaults to False.

• output_path (str, optional): The path to save the output plot. Defaults to None.

• plt_show (bool, optional): Whether to show the plot. Defaults to False.

Returns:

• None

buscoplotpy.graphics.synteny.plot_chromosomes(chromosomes: dict, fig: Figure, ax: Axes) → None

Plots the chromosomes on the given axes.

Parameters:

• chromosomes (dict): Dictionary mapping sequence names to Chromosome objects.

• ax (plt.Axes): Matplotlib axes object to plot the chromosomes on.

Returns:

• None

buscoplotpy.graphics.synteny.plot_links(links: list, ax: Axes) → None

Plots the links on the given axes.

Parameters:

• links (list): List of Link objects.

• ax (plt.Axes): Matplotlib axes object to plot the links on.

Returns:

• None

buscoplotpy.graphics.synteny.vertical_synteny_plot(ft_1: DataFrame, ft_2: DataFrame, karyotype_1: DataFrame, karyotype_2: DataFrame, title: str = 'Synteny plot', dim: int = 2, figsize=(18, 10), dpi: int = 300, round_edges: bool = False, link_colors: dict = {}, straight_line: bool = False, output_path: str = None, bbox_inches: str = 'tight', plt_show: bool = False)

Generate a vertical synteny plot.

Parameters:

• ft_1 (pd.DataFrame): Full table for the left karyotype.

• ft_2 (pd.DataFrame): Full table for the right karyotype.

• karyotype_1 (pd.DataFrame): Karyotype dataframe for the left karyotype.

• karyotype_2 (pd.DataFrame): Karyotype dataframe for the right karyotype.

• title (str, optional): The title of the plot. Defaults to ‘Synteny plot’.

• dim (int, optional): The dimension of the chromosomes. Defaults to 2.

• figsize (tuple, optional): The size of the plot figure. Defaults to (18, 10).

• dpi (int, optional): The resolution of the plot figure. Defaults to 300.

• round_edges (bool, optional): Whether to round the edges of the karyotype blocks. Defaults to False.

• link_colors (dict, optional): A dictionary mapping link colors to chromosome pairs. Defaults to {}.

• straight_line (bool, optional): Whether to use straight lines for links. Defaults to False.

• output_path (str, optional): The path to save the plot to. Defaults to None.

• plt_show (bool, optional): Whether to show the plot. Defaults to False.

Returns:

• None

Module contents