SystemsPartitionVisualizer#

class panorama.systems.systems_partitions.SystemsPartitionVisualizer(name, output_dir, formats=None)#

Bases: VisualizationBuilder

Visualizer for pangenome systems partition distributions.

This class creates heatmap visualizations showing how pangenome systems are partitioned (persistent, shell, cloud, etc.) across different organisms. The visualization helps understand the conservation patterns of genetic systems.

partitions#

List of partition categories

partition2color#

Mapping from partitions to colors

mapper#

Categorical color mapper for partitions

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 SystemsPartitionVisualizer.

Parameters:

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

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

  • formats (Optional[List[str]]) – List of output formats to generate

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_bar_plots(partition_matrix)#

Create bar plots showing system and organism statistics.

Creates stacked bars for partition distributions (left) and organism counts (top) to provide marginal summaries of the partition matrix.

Parameters:

partition_matrix (DataFrame) – DataFrame with partition information

Return type:

None

create_color_bar(title)#

Create a color bar for the partition matrix.

Parameters:

title (str) – Title to display on the color bar

Return type:

None

create_left_bar(source)#

Create a stacked horizontal bar plot showing partition distributions by system.

Parameters:

source (ColumnDataSource) – ColumnDataSource containing stacked partition data

Return type:

None

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

create_main_figure(partition_matrix, x_range, y_range)#

Create the main partition matrix heatmap figure.

Parameters:

  • partition_matrix (DataFrame) – DataFrame with systems, organisms, and partition information

  • x_range (FactorRange) – X-axis range for the plot (organisms)

  • y_range (FactorRange) – Y-axis range for the plot (systems)

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.

plot()#

Create and save the complete partition visualization layout.

Arranges the main partition heatmap with supporting bar plots and color bar in a clean grid layout, then saves the result in specified formats.

Return type:

None

property top_bar: figure#

Get the top bar plot figure.