VisualizationBuilder#

class panorama.systems.utils.VisualizationBuilder(name, output_dir, formats=None)#

Bases: ABC

Abstract base class for building correlation matrix and partition visualizations.

This class maintains a common configuration and provides a cohesive interface for creating all components of pangenome visualizations. It handles shared functionality like plot dimensions, styling, and file saving.

BELOW_HEIGHT = 138#

Space for bottom plots

Type:

int

CENTER_WIDTH = 1335#

Space for main heatmap

Type:

int

DEFAULT_FORMAT = 'html'#

Default output format when none specified

Type:

str

LEFT_WIDTH = 267#

Space for left bar plots

Type:

int

MIDDLE_HEIGHT = 644#

Space for main heatmap

Type:

int

OUTPUT_FORMATS = ['html', 'png']#

Supported output formats for saving figures

Type:

list

PNG_EXPORT_HEIGHT = 1080#

Height of PNG exports

Type:

int

PNG_EXPORT_WIDTH = 1920#

Width of PNG exports

Type:

int

RIGHT_WIDTH = 178#

Space for color bars

Type:

int

TOP_HEIGHT = 138#

int Space for top bar plots

TOTAL_HEIGHT = 920#

Total height of the complete visualization layout.

Type:

int

TOTAL_WIDTH = 1780#

Total width of the complete visualization layout.

Type:

int

__init__(name, output_dir, formats=None)#

Initialize the visualization builder.

Parameters:

  • name (str) – Name of the pangenome for visualization titles and filenames

  • output_dir (Path) – Directory path where output files will be saved

  • formats (Optional[List[str]]) – List of output formats to generate. Defaults to [“html”]

static _configure_bar_plot_style(plot, x_label=None, y_label=None, flip_x=False, hide_x_axis=False, hide_y_axis=False)#

Configure styling for bar plots.

Parameters:

  • plot (figure) – The figure to configure

  • x_label (Optional[str]) – Label for x-axis

  • y_label (Optional[str]) – Label for y-axis

  • flip_x (bool) – Whether to flip the x-axis

  • hide_x_axis (bool) – Whether to hide the x-axis

  • hide_y_axis (bool) – Whether to hide the y-axis

Return type:

None

static _configure_minimal_plot(plot)#

Configure a minimal plot style (no axes, grid, etc.).

Parameters:

plot (figure) – The figure to configure with minimal styling

Return type:

None

_configure_plot_style()#

Configure common plot styling for the main figure.

This method sets up consistent appearance across all visualization types, including fonts, colors, and axis properties.

Return type:

None

_create_main_figure(matrix, x_range=None, y_range=None, tooltips=None)#

Create the main heatmap figure with common configuration.

Parameters:

  • matrix (DataFrame) – Data matrix for determining ranges if not provided

  • x_range (Optional[FactorRange]) – X-axis range for the plot. If None, derived from matrix columns

  • y_range (Optional[FactorRange]) – Y-axis range for the plot. If None, derived from matrix index

  • tooltips (Optional[List[Tuple[str, str]]]) – List of tooltip specifications as (label, field) tuples

Return type:

None

_save_figure(fig, filename_base)#

Save a Bokeh figure in the specified formats.

Parameters:

  • fig (figure) – The Bokeh figure object to save

  • filename_base (str) – Base filename without extension

Raises:

Exception – If an unsupported output format is specified

Return type:

None

property color_bar: figure#

Get the color bar figure.

create_left_bar_plot(source, matrix, y_field='system_name', value_field='count', color='navy')#

Create a horizontal bar plot on the left side of the visualization.

Parameters:

  • source (ColumnDataSource) – ColumnDataSource containing the data for the bars

  • matrix (DataFrame) – Data matrix for determining the y-range

  • y_field (str) – Field name for the y-axis values

  • value_field (str) – Field name for the bar values

  • color (str) – Color for the bars

Return type:

None

abstractmethod create_main_figure(*args, **kwargs)#

Create the main visualization figure.

This method must be implemented by subclasses to create their specific type of main visualization (correlation matrix, partition matrix, etc.).

Return type:

None

create_top_bar_plot(source, x_field, value_field='count', color='green', x_order=None)#

Create a vertical bar plot on the top of the visualization.

Parameters:

  • source (ColumnDataSource) – ColumnDataSource containing the data for the bars

  • x_field (str) – Field name for the x-axis values

  • value_field (str) – Field name for the bar values

  • color (str) – Color for the bars

  • x_order (Optional[List[str]]) – Custom ordering for x-axis. If None, uses source data order

Return type:

None

property glyph: Glyph#

Get the glyph from the renderer.

property glyph_renderer: GlyphRenderer#

Get the glyph renderer for the main plot.

property left_bar: figure#

Get the left bar plot figure.

property main_plot: figure#

Get the main heatmap plot figure.

abstractmethod plot()#

Create and save the complete visualization layout.

This method must be implemented by subclasses to define their specific layout arrangement and save the final visualization.

Return type:

None

property top_bar: figure#

Get the top bar plot figure.