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Visualizing Networks in RISK

Visualization highlights clusters within the network to make modular structure and functional associations easier to interpret. RISK provides a flexible and powerful plotting interface via the NetworkPlotter object. This enables generation of publication-ready figures with detailed domain annotations, significance-driven coloring, contours, and rich label customization.

Create a NetworkPlotter

Load your NetworkGraph object into a NetworkPlotter.

Parameters:

  • graph (NetworkGraph): The NetworkGraph object containing the network structure to be visualized.
  • figsize (tuple, optional): Size of the figure, specified as a tuple (width, height) in inches. Defaults to (10, 10).
  • background_color (str, list, tuple, or np.ndarray, optional): Background color of the plot. Provide a single color (e.g., 'white', (1.0, 1.0, 1.0) for RGB, or (1.0, 1.0, 1.0, 1.0) for RGBA). Defaults to 'white'.
  • background_alpha (float, None, optional): Transparency level of the background color. If provided, it overrides any existing alpha values found in background_color. Defaults to 1.0.
  • pad (float, optional): Padding value to adjust the axis limits around the network plot. Defaults to 0.3.

Returns: NetworkPlotter: An instance of the plotter initialized with the provided graph and settings.

plotter = risk.load_plotter(
    graph=graph,
    figsize=(15, 15),
    background_color="black",
    background_alpha=1.0,
    pad=0.3,
)

plot_title()

Add a title and optional subtitle overlay.

Parameters:

  • title (str, optional): Title of the plot. Defaults to None.
  • subtitle (str, optional): Subtitle of the plot. Defaults to None.
  • title_fontsize (int, optional): Font size for the title. Defaults to 20.
  • subtitle_fontsize (int, optional): Font size for the subtitle. Defaults to 14.
  • font (str, optional): Font family used for both the title and subtitle. Defaults to "DejaVu Sans".
  • title_color (str, list, tuple, or np.ndarray, optional): Color of the title text. Provide a single color (e.g., "black", (0.0, 0.0, 0.0) for RGB, or (0.0, 0.0, 0.0, 1.0) for RGBA). Defaults to "black".
  • title_color (str, list, tuple, or np.ndarray, optional): Color of the subtitle text. Provide a single color (e.g., "black", (0.0, 0.0, 0.0) for RGB, or (0.0, 0.0, 0.0, 1.0) for RGBA). Defaults to "black".
  • title_x (float, optional): X-axis position of the title. Defaults to 0.5.
  • title_y (float, optional): Y-axis position of the title. Defaults to 0.975.
  • title_space_offset (float, optional): Fraction of figure height to leave for the space above the plot. Defaults to 0.075.
  • subtitle_offset (float, optional): Offset factor to position the subtitle below the title. Defaults to 0.025.
plotter.plot_title(
    title="Yeast PPI Network",
    subtitle="Michaelis et al., 2023",
    title_fontsize=24,
    subtitle_fontsize=18,
    font="Arial",
    title_color="white",
    subtitle_color="lightblue",
    title_x=0.5,
    title_y=0.925,
    title_space_offset=0.08,
    subtitle_offset=0.025,
)

plot_circle_perimeter()

Draw a circular boundary around the network layout.

Parameters:

  • scale (float, optional): Scaling factor for the perimeter's diameter. Defaults to 1.0.
  • center_offset_x (float, optional): Horizontal offset as a fraction of the diameter. Negative values shift the center left, positive values shift it right. Defaults to 0.0.
  • center_offset_y (float, optional): Vertical offset as a fraction of the diameter. Negative values shift the center down, positive values shift it up. Defaults to 0.0.
  • linestyle (str, optional): Line style for the circle. Options include "solid", "dashed", "dashdot", "dotted", or any Matplotlib-supported linestyle. Defaults to "dashed".
  • linewidth (float, optional): Width of the circle's outline. Defaults to 1.5.
  • color (str, list, tuple, or np.ndarray, optional): Color of the circle. Provide a single color (e.g., "black", (0.0, 0.0, 0.0) for RGB, or (0.0, 0.0, 0.0, 1.0) for RGBA). Defaults to "black".
  • outline_alpha (float, None, optional): Transparency level for the circle's outline. If provided, it overrides any existing alpha values found in color. Defaults to 1.0.
  • fill_alpha (float, None, optional): Transparency level for the circle’s fill. If provided, it overrides any existing alpha values found in color. Defaults to 0.0.
plotter.plot_circle_perimeter(
    scale=1.02,
    center_offset_x=0.0,
    center_offset_y=0.0,
    linestyle="solid",
    linewidth=1.5,
    color="white",
    outline_alpha=1.0,
    fill_alpha=0.0,
)

For a more flexible contour-based layout boundary, see plot_contour_perimeter().

plot_contour_perimeter()

Draw a contour boundary around the network layout.

Parameters:

  • scale (float, optional): Scaling factor for the perimeter size. Defaults to 1.0.
  • levels (int, optional): Number of contour levels. Defaults to 3.
  • bandwidth (float, optional): Bandwidth for KDE, controlling the smoothness of the contour. Defaults to 0.8.
  • grid_size (int, optional): Resolution of the grid for KDE. Higher values create finer contours. Defaults to 250.
  • color (str, list, tuple, or np.ndarray, optional): Color of the circle. Provide a single color (e.g., "black", (0.0, 0.0, 0.0) for RGB, or (0.0, 0.0, 0.0, 1.0) for RGBA). Defaults to "black".
  • linestyle (str, optional): Line style for the contour. Options include "solid", "dashed", "dashdot", "dotted", or any Matplotlib-supported linestyle. Defaults to "solid".
  • linewidth (float, optional): Width of the contour’s outline. Defaults to 1.5.
  • outline_alpha (float, None, optional): Transparency level for the contour's outline. If provided, it overrides any existing alpha values found in color. Defaults to 1.0.
  • fill_alpha (float, None, optional): Transparency level for the contour’s fill. If provided, it overrides any existing alpha values found in color. Defaults to 0.0.
plotter.plot_contour_perimeter(
    levels=5,
    bandwidth=0.8,
    grid_size=250,
    color="white",
    linestyle="solid",
    linewidth=2.0,
    alpha=1.0,
    fill_alpha=0.2,
)

plot_network()

Render nodes and edges with styles derived from significance-aware helpers.

Parameters:

  • node_size (int or np.ndarray, optional): Size of the nodes. Can be a single integer or an array of sizes. Defaults to 50.
  • node_shape (str, optional): Shape of the nodes. Options include:
    • 'o': Circle. (default)
    • 's': Square.
    • '^': Triangle up.
    • 'v': Triangle down.
    • Other options: 'p', 'P', 'h', 'H', '8', 'd', 'D', '>', '<, '|', '_'.
  • node_edgewidth (float, optional): Width of the edges around each node. Defaults to 1.0.
  • edge_width (float, optional): Width of the edges in the plot. Defaults to 1.0.
  • node_color (str, list, tuple, or np.ndarray, optional): Color of the nodes. Can be a single color (e.g., "white", "red", (0.5, 0.5, 0.5) for RGB, or (0.5, 0.5, 0.5, 0.8) for RGBA) or an array of such colors. Defaults to "white".
  • node_edgecolor (str, list, tuple, or np.ndarray, optional): Color of the edges around each node. Can be a single color, a string of colors, or an array of string or RGB/RGBA colors. Defaults to "black".
  • edge_color (str, list, tuple, or np.ndarray, optional): Color of the edges connecting the nodes. Can be a single color, a string of colors, or an array of string or RGB/RGBA colors. Defaults to "black".
  • node_alpha (float or None, optional): Alpha value (transparency) for the nodes. Range: 0.0 (fully transparent) to 1.0(fully opaque). If provided, it overrides any alpha values innode_color`. Defaults to 1.0.
  • edge_alpha (float or None, optional): Alpha value (transparency) for the edges. Range: 0.0 (fully transparent) to 1.0(fully opaque). If provided, it overrides any alpha values inedge_color`. Defaults to 1.0.
plotter.plot_network(
    node_size=node_sizes,
    node_color=node_colors,
    node_shape="o",
    node_edgewidth=1.0,
    edge_width=0.03,
    node_edgecolor="black",
    edge_color="white",
    node_alpha=1.0,
    edge_alpha=1.0,
)

get_annotated_node_sizes()

Generate node sizes based on annotation significance.

Parameters:

  • singificant_size (int, optional): Size for singificant nodes. Defaults to 50.
  • nonsignificant_size (int, optional): Size for non-singificant nodes. Defaults to 25.

Returns: list: List of node sizes corresponding to graph nodes.

node_sizes = plotter.get_annotated_node_sizes(
    significant_size=225,
    nonsignificant_size=12.5,
)

get_annotated_node_colors()

Generate node colors based on annotation significance and optional blending.

Parameters:

  • cmap (str, optional): The colormap to use for node colors. Defaults to "gist_rainbow".
  • color (str, list, tuple, np.ndarray, or None, optional): A specific color to use for all nodes. Can be a single color (e.g., "red", (0.5, 0.5, 0.5) for RGB, or (0.5, 0.5, 0.5, 0.8) for RGBA) or an array of such colors. If specified, this will override the colormap (cmap). Defaults to None.
  • blend_colors (bool, optional): Whether to blend colors for nodes with multiple domains. Defaults to False.
  • blend_gamma (float, optional): Gamma correction factor for perceptual color blending. Defaults to 2.2.
  • min_scale (float, optional): Minimum scale for color intensity. Defaults to 0.8.
  • max_scale (float, optional): Maximum scale for color intensity. Defaults to 1.0.
  • scale_factor (float, optional): Factor for adjusting the color scaling intensity. Defaults to 1.0.
  • alpha (float, None, optional): Alpha value for singificant nodes. If provided, it overrides any existing alpha values found in color. Defaults to 1.0.
  • nonsignificant_color (str, list, tuple, or np.ndarray, optional): Color for non-singificant nodes. Can be a single color (e.g., "white", (0.5, 0.5, 0.5) for RGB, or (0.5, 0.5, 0.5, 0.8) for RGBA) or an array of such colors. Defaults to "white".
  • nonsignificant_alpha (float, None, optional): Alpha value for non-singificant nodes. If provided, it overrides any existing alpha values found in nonsignificant_color. Defaults to 1.0.
  • ids_to_colors (dict, None, optional): Mapping of domain IDs to specific colors. Defaults to None.
  • random_seed (int, optional): Seed for random number generation. Defaults to 888.

Returns: list: List of colors for each node.

node_colors = plotter.get_annotated_node_colors(
    cmap="gist_rainbow",
    color=None,
    blend_colors=False,
    blend_gamma=2.2,
    min_scale=1.0,
    max_scale=1.0,
    scale_factor=0.5,
    alpha=1.0,
    nonsignificant_color="white",
    nonsignificant_alpha=0.75,
    ids_to_colors=None,
    random_seed=887,
)

plot_subnetwork()

Overlay a selected group of nodes and their connecting edges with distinct styling.

Parameters:

  • nodes (list, tuple, or np.ndarray): List of node labels to include in the subnetwork. Accepts nested lists.
  • node_size (int or np.ndarray, optional): Size of the nodes. Can be a single integer or an array of sizes. Defaults to 50.
  • node_shape (str, optional): Shape of the nodes. Options include:
    • 'o': Circle. (default)
    • 's': Square.
    • '^': Triangle up.
    • 'v': Triangle down.
    • Other options: 'p', 'P', 'h', 'H', '8', 'd', 'D', '>', '<, '|', '_'.
  • node_edgewidth (float, optional): Width of the node edges. Defaults to 1.0.
  • edge_width (float, optional): Width of the edges in the subnetwork plot. Defaults to 1.0.
  • node_color (str, list, tuple, or np.ndarray, optional): Color of the nodes. Can be a single color (e.g., "red", (0.5, 0.5, 0.5) for RGB, or (0.5, 0.5, 0.5, 0.8) for RGBA) or an array of such colors. Defaults to "white".
  • node_edgecolor (str, list, tuple, or np.ndarray, optional): Color of the node edges. Can be a single color or an array of string or RGB/RGBA colors. Defaults to "black".
  • edge_color (str, list, tuple, or np.ndarray, optional): Color of the edges connecting the nodes. Can be a single color or an array of string or RGB/RGBA colors. Defaults to "black".
  • node_alpha (float or None, optional): Transparency for the nodes. Range: 0.0 (fully transparent) to 1.0 (fully opaque). If provided, it overrides any alpha values in node_color. Defaults to None.
  • edge_alpha (float or None, optional): Transparency for the edges. Range: 0.0 (fully transparent) to 1.0 (fully opaque). If provided, it overrides any alpha values in edge_color. Defaults to None.
plotter.plot_subnetwork(
    nodes=[
        "LSM1", "LSM2", "LSM3", "LSM4", "LSM5", "LSM6", "LSM7", "PAT1",
    ],
    node_size=225,
    node_shape="^",
    node_edgewidth=1.0,
    edge_width=0.04,
    node_color="white",
    node_edgecolor="black",
    edge_color="white",
    node_alpha=1.0,
    edge_alpha=1.0,
)

plot_contours()

Draw contours for domains (e.g., GO term regions).

Parameters:

  • levels (int, optional): Number of contour levels to plot. Defaults to 5.
  • bandwidth (float, optional): Bandwidth for KDE, controlling the smoothness of the contour. Defaults to 0.8.
  • grid_size (int, optional): Resolution of the grid for KDE. Higher values create finer contours. Defaults to 250.
  • color (str, list, tuple, or np.ndarray, optional): Color of the contours. Can be a string (e.g., "white"), an RGB/RGBA value, or an array of such values. Defaults to "white".
  • linestyle (str, optional): Line style for the contours. Options include 'solid', 'dashed', 'dashdot', `'dotted'. Defaults to "solid".
  • linewidth (float, optional): Line width for the contours. Defaults to 1.5.
  • alpha (float, None, optional): Transparency level of the contour lines. Range: 0.0 (fully transparent) to 1.0 (fully opaque). If provided, it overrides any existing alpha values found in color. Defaults to 1.0.
  • fill_alpha (float, None, optional): Transparency level of the contour fill. If provided, it overrides any existing alpha values found in color. Defaults to None.
plotter.plot_contours(
    levels=5,
    bandwidth=0.8,
    grid_size=250,
    color=plotter.get_annotated_contour_colors(
        cmap="gist_rainbow",
        color=None,
        blend_colors=False,
        blend_gamma=2.2,
        min_scale=1.0,
        max_scale=1.0,
        scale_factor=0.5,
        ids_to_colors=None,
        random_seed=887,
    ),
    linestyle="solid",
    linewidth=2.0,
    alpha=1.0,
    fill_alpha=0.2,
)

get_annotated_contour_colors()

Generate colors for domain contours based on annotation significance.

Parameters:

  • cmap (str, optional): The colormap to use for contour colors. Defaults to "gist_rainbow".
  • color (str, list, tuple, np.ndarray, or None, optional): A specific color to use for all contours. Can be a string (e.g., "red"), an RGB or RGBA value, or an array of such values (strings, RGB, or RGBA). If specified, this will overwrite the colormap (cmap). Defaults to None.
  • blend_colors (bool, optional): Whether to blend colors for nodes with multiple domains. Defaults to False.
  • blend_gamma (float, optional): Gamma correction factor for perceptual color blending. Defaults to 2.2.
  • min_scale (float, optional): Minimum intensity scale for the colors generated by the colormap. Controls the dimmest colors. Defaults to 0.8.
  • max_scale (float, optional): Maximum intensity scale for the colors generated by the colormap. Controls the brightest colors. Defaults to 1.0.
  • scale_factor (float, optional): Exponent for adjusting color scaling based on significance scores. A higher value increases contrast by dimming lower scores more. Defaults to 1.0.
  • ids_to_colors (dict, None, optional): Mapping of domain IDs to specific colors. Defaults to None.
  • random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.

Returns: list: List of colors for each domain contour.

contour_colors = plotter.get_annotated_contour_colors(
    cmap="gist_rainbow",
    color=None,
    blend_colors=False,
    blend_gamma=2.2,
    min_scale=1.0,
    max_scale=1.0,
    scale_factor=0.5,
    ids_to_colors=None,
    random_seed=887,
)

plot_subcontour()

Draw a contour around a subset of nodes.

Parameters:

  • nodes (list, tuple, or np.ndarray): List of node labels or list of lists of node labels to plot the contour for.
  • levels (int, optional): Number of contour levels to plot. Defaults to 5.
  • bandwidth (float, optional): Bandwidth for KDE, controlling the smoothness of the contour. Defaults to 0.8.
  • grid_size (int, optional): Resolution of the grid for KDE. Higher values create finer contours. Defaults to 250.
  • color (str, list, tuple, or np.ndarray, optional): Color of the contour. Can be a string (e.g., "white"), an RGB or RGBA value, or an array of such values (strings, RGB, or RGBA). Defaults to "white".
  • linestyle (str, optional): Line style for the contour. Options include 'solid', 'dashed', 'dashdot', 'dotted'. Defaults to "solid".
  • linewidth (float, optional): Line width for the contour. Defaults to 1.5.
  • alpha (float, None, optional): Transparency level of the contour lines. Range: 0.0 (fully transparent) to 1.0(fully opaque). If provided, it overrides any existing alpha values found incolor`. Defaults to 1.0.
  • fill_alpha (float, None, optional): Transparency level of the contour fill. If provided, it overrides any existing alpha values found in color. Defaults to None.
plotter.plot_subcontour(
    nodes=[
        "LSM1", "LSM2", "LSM3", "LSM4", "LSM5", "LSM6", "LSM7", "PAT1",
    ],
    levels=5,
    bandwidth=0.8,
    grid_size=250,
    color="white",
    linestyle="solid",
    linewidth=2.0,
    alpha=1.0,
    fill_alpha=0.25,
)

plot_labels()

Annotate selected nodes or domains with styled text and arrows.

Parameters:

  • scale (float, optional): Scale factor for positioning labels around the perimeter. Defaults to 1.05.
  • offset (float, optional): Offset distance for labels from the perimeter. Defaults to 0.10.
  • font (str, optional): Font name for the labels. Defaults to "DejaVu Sans".
  • fontcase (str, dict, or None, optional): Defines how to transform the case of words. Can be a string ('upper', 'lower', 'title') or a dictionary mapping cases (e.g., {'lower': 'title', 'upper': 'lower'}). Defaults to None.
  • fontsize (int, optional): Font size for the labels. Defaults to 10.
  • fontcolor (str, list, tuple, or np.ndarray, optional): Color of the label text. Can be a string (e.g., "black"), an RGB or RGBA value, or an array of such values (strings, RGB, or RGBA). Defaults to "black".
  • fontalpha (float, None, optional): Transparency level for the font color. Range: 0.0 (fully transparent) to 1.0 (fully opaque). If provided, it overrides any existing alpha values found in fontcolor. Defaults to 1.0.
  • arrow_linewidth (float, optional): Line width of the arrows pointing to centroids. Defaults to 1.
  • arrow_style (str, optional): Style of the arrows pointing to centroids. Defaults to "->".
  • arrow_color (str, list, tuple, or np.ndarray, optional): Color of the arrows. Can be a string (e.g., "black"), an RGB or RGBA value, or an array of such values (strings, RGB, or RGBA). Defaults to "black".
  • arrow_alpha (float, None, optional): Transparency level for the arrow color. Range: 0.0 (fully transparent) to 1.0 (fully opaque). If provided, it overrides any existing alpha values found in arrow_color. Defaults to 1.0.
  • arrow_base_shrink (float, optional): Distance between the text and the base of the arrow. Defaults to 0.0.
  • arrow_tip_shrink (float, optional): Distance between the arrow tip and the centroid. Defaults to 0.0.
  • max_labels (int, optional): Maximum number of labels to plot. Defaults to None` (no limit.
  • min_label_lines (int, optional): Minimum number of lines in a label. Defaults to 1.
  • max_label_lines (int, optional): Maximum number of lines in a label. Defaults to None` (no limit.
  • min_chars_per_line (int, optional): Minimum number of characters in a line to display. Defaults to 1.
  • max_chars_per_line (int, optional): Maximum number of characters in a line to display. Defaults to None (no limit).
  • words_to_omit (list, optional): List of words to omit from the labels. Defaults to None.
  • overlay_ids (bool, optional): Whether to overlay domain IDs in the center of the centroids. Defaults to False.
  • ids_to_keep (list, tuple, np.ndarray, or None, optional): IDs of domains that must be labeled. To discover domain IDs, you can set overlay_ids=True. Defaults to None.
  • ids_to_labels (dict, optional): A dictionary mapping domain IDs to custom labels (strings). The labels should be space-separated words. If provided, the custom labels will replace the default domain terms. Defaults to None.
plotter.plot_labels(
    scale=1.1,
    offset=0.12,
    font="Arial",
    fontcase={"title": "lower"},
    fontsize=15,
    fontcolor="white",
    fontalpha=1.0,
    arrow_linewidth=2.0,
    arrow_style="-",
    arrow_color=plotter.get_annotated_label_colors(
        cmap="gist_rainbow",
        color=None,
        blend_colors=False,
        blend_gamma=2.2,
        min_scale=1.0,
        max_scale=1.0,
        scale_factor=0.5,
        ids_to_colors=None,
        random_seed=887,
    ),
    arrow_alpha=1.0,
    arrow_base_shrink=10.0,
    arrow_tip_shrink=0.0,
    max_labels=28,
    min_label_lines=3,
    max_label_lines=4,
    min_chars_per_line=3,
    max_chars_per_line=12,
    words_to_omit=["from", "the", "into", "via", "novo", "process", "activity"],
    overlay_ids=False,
    ids_to_keep=None,
    ids_to_labels=None,
)

get_annotated_label_colors()

Generate colors for labels based on annotation significance.

Parameters:

  • cmap (str, optional): The colormap to use for label colors. Defaults to "gist_rainbow".
  • color (str, list, tuple, np.ndarray, or None, optional): A specific color to use for all labels. Can be a string (e.g., "red"), an RGB or RGBA value, or an array of such values (strings, RGB, or RGBA). Warning: If specified, this will overwrite the colormap (cmap). Defaults to None.
  • blend_colors (bool, optional): Whether to blend colors for nodes with multiple domains. Defaults to False.
  • blend_gamma (float, optional): Gamma correction factor for perceptual color blending. Defaults to 2.2.
  • min_scale (float, optional): Minimum intensity scale for the colors generated by the colormap. Controls the dimmest colors. Defaults to 0.8.
  • max_scale (float, optional): Maximum intensity scale for the colors generated by the colormap. Controls the brightest colors. Defaults to 1.0.
  • scale_factor (float, optional): Exponent for adjusting color scaling based on significance scores. A higher value increases contrast by dimming lower scores more. Defaults to 1.0.
  • ids_to_colors (dict, None, optional): Mapping of domain IDs to specific colors. Defaults to None.
  • random_seed (int, optional): Seed for random number generation to ensure reproducibility. Defaults to 888.

Returns: list: List of colors for each label.

label_colors = plotter.get_annotated_label_colors(
    cmap="gist_rainbow",
    color=None,
    blend_colors=False,
    blend_gamma=2.2,
    min_scale=1.0,
    max_scale=1.0,
    scale_factor=0.5,
    ids_to_colors=None,
    random_seed=887,
)

plot_sublabel()

Add a single label tied to a chosen set of nodes (arrow points to centroid). Useful for naming complexes or pathway modules.

Parameters:

  • nodes (list, tuple, or np.ndarray): List of node labels or list of lists of node labels to be used for calculating the centroid.
  • label (str): The label to be annotated on the network.
  • radial_position (float, optional): Radial angle for positioning the label around the network's perimeter. Range: 0-360 degrees. Defaults to 0.0.
  • scale (float, optional): Scale factor for positioning the label around the perimeter. Defaults to 1.05.
  • offset (float, optional): Offset distance for the label from the perimeter. Defaults to 0.10.
  • font (str, optional): Font name for the label. Defaults to "DejaVu Sans".
    • Options: Any valid font name (e.g., "DejaVu Sans", "Times New Roman").
  • fontsize (int, optional): Font size for the label. Defaults to 10.
    • Options: Any integer value representing font size.
  • fontcolor (str, list, tuple, or np.ndarray, optional): Color of the label text. Can be a string (e.g., "black"), an RGB or RGBA value, or an array of such values. Defaults to "black".
  • fontalpha (float, None, optional): Transparency level for the label font. Range: 0.0 (fully transparent) to 1.0 (fully opaque). If provided, it overrides any existing alpha values found in fontcolor. Defaults to 1.0.
  • arrow_linewidth (float, optional): Line width of the arrow pointing to the centroid. Defaults to 1.
  • arrow_style (str, optional): Style of the arrows pointing to the centroid. Defaults to "->".
  • arrow_color (str, list, tuple, or np.ndarray, optional): Color of the arrow. Can be a string, RGB/RGBA value, or an array of such values. Defaults to "black".
  • arrow_alpha (float, None, optional): Transparency level for the arrow. Range: 0.0 (fully transparent) to 1.0 (fully opaque). If provided, it overrides any existing alpha values found in arrow_color. Defaults to 1.0.
  • arrow_base_shrink (float, optional): Distance between the text and the base of the arrow. Defaults to 0.0.
  • arrow_tip_shrink (float, optional): Distance between the arrow tip and the centroid. Defaults to 0.0.
plotter.plot_sublabel(
    nodes=[
        "LSM1", "LSM2", "LSM3", "LSM4", "LSM5", "LSM6", "LSM7", "PAT1",
    ],
    label="LSM1-7-PAT1 Complex",
    radial_position=73,
    scale=1.6,
    offset=0.12,
    font="Arial",
    fontsize=15,
    fontcolor="white",
    fontalpha=1.0,
    arrow_linewidth=2.0,
    arrow_style="-",
    arrow_color="white",
    arrow_alpha=1.0,
    arrow_base_shrink=10.0,
    arrow_tip_shrink=0.0,
)

savefig()

Save the current figure to file in formats like PNG, SVG, or PDF.

Parameters:

  • *args: Positional arguments passed to plt.savefig. Commonly used for specifying the filename (e.g., "plot.png").
  • pad_inches (float, optional): Padding around the figure when saving. Defaults to 0.5.
  • dpi (int, optional): Dots per inch (DPI) for the exported image. Defaults to 100.
  • **kwargs: Keyword arguments passed to plt.savefig, such as format (e.g., "png", "pdf") and other options like bbox_inches.
plotter.savefig("my_plot.png", pad_inches=0.5, dpi=100)

show()

Display the current figure inline or in a graphical window.

Parameters:

  • *args: Positional arguments passed to plt.show. Typically not used, but can be included for consistency.
  • **kwargs: Keyword arguments passed to plt.show, such as block to control whether the display blocks the execution of code.
plotter.show()

Annotated Yeast PPI Network

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Overview of risk.params