Settings and properties

canvas_width

canvas_width -> int

Property that returns the current canvas width in pixels.

Returns:

  • int: Current canvas width

Example:

# Get current canvas width
width = gw.canvas_width
print(f"Canvas width: {width}px")

set_canvas_width

set_canvas_width(width: int) -> 'Gw'

Set the canvas width and recreate the raster surface.

Parameters:

  • width (int): New canvas width in pixels

Returns:

  • Gw: Self for method chaining

canvas_height

canvas_height -> int

Property that returns the current canvas height in pixels.

Returns:

  • int: Current canvas height

Example:

# Get current canvas height
height = gw.canvas_height
print(f"Canvas height: {height}px")

set_canvas_height

set_canvas_height(height: int) -> 'Gw'

Set the canvas height and recreate the raster surface.

Parameters:

  • height (int): New canvas height in pixels

Returns:

  • Gw: Self for method chaining

canvas_size

canvas_size -> Tuple[int, int]

Property that returns the current canvas dimensions.

Returns:

  • tuple: (width, height) in pixels

Example:

# Get current canvas dimensions
width, height = gw.canvas_size
print(f"Canvas dimensions: {width}x{height}px")

set_canvas_size

set_canvas_size(width: int, height: int) -> 'Gw'

Set both canvas width and height and recreate the raster surface.

Parameters:

  • width (int): New canvas width in pixels
  • height (int): New canvas height in pixels

Returns:

  • Gw: Self for method chaining

theme

theme -> str

Property that returns the current theme name.

Returns:

  • str: Current theme name (“slate”, “dark”, or “igv”)

Example:

# Get current theme
theme = gw.theme
print(f"Current theme: {theme}")

set_theme

set_theme(theme_name: str) -> 'Gw'

Set a predefined visualisation theme.

Parameters:

  • theme_name (str): Theme name, must be one of “slate”, “dark”, or “igv”

Returns:

  • Gw: Self for method chaining

Raises:

  • ValueError: If theme_name is not one of the supported themes

Example:

# Set the dark theme
gw.set_theme("dark")

set_paint_ARBG

set_paint_ARBG(paint_enum: int, a: int, r: int, g: int, b: int) -> 'Gw'

Set the ARGB color for a specific paint type.

Parameters:

  • paint_enum (int): Paint type enumeration value from GwPalette enum or Paint class (e.g., GwPalette.NORMAL_READ, GwPalette.DELETION)
  • a (int): Alpha channel value (0-255)
  • r (int): Red channel value (0-255)
  • g (int): Green channel value (0-255)
  • b (int): Blue channel value (0-255)

Returns:

  • Gw: Self for method chaining

Example:

# Set normal read color to dark blue
gw.set_paint_ARBG(GwPalette.NORMAL_READ, 255, 0, 0, 128)

apply_theme

apply_theme(theme_dict: Dict[int, Tuple[int, int, int, int]]) -> 'Gw'

Apply a custom theme using a dictionary of paint types and colors.

Parameters:

  • theme_dict (dict): Dictionary mapping Paint constants to ARGB tuples (alpha, red, green, blue)

Returns:

  • Gw: Self for method chaining

Example:

custom_theme = {
    GwPalette.BACKGROUND: (255, 240, 240, 240),
    GwPalette.NORMAL_READ: (255, 100, 100, 100),
    GwPalette.DELETION: (255, 255, 0, 0)
}
gw.apply_theme(custom_theme)

load_theme_from_json

load_theme_from_json(filepath: str) -> 'Gw'

Load and apply a theme from a JSON file.

Parameters:

  • filepath (str): Path to the JSON theme file

Returns:

  • Gw: Self for method chaining

Raises:

  • ValueError: If the color name is not recognised

Example:

gw.load_theme_from_json("custom_theme.json")

save_theme_to_json

save_theme_to_json(filepath: str) -> 'Gw'

Save the current theme settings to a JSON file.

This function exports all paint colors from the current theme to a JSON file that can later be loaded with load_theme_from_json.

Parameters:

  • filepath (str): Path where the JSON theme file should be saved

Returns:

  • Gw: Self for method chaining

Example:

# Save the current theme for future use
gw.save_theme_to_json("my_theme.json")

font_size

font_size -> int

Property that returns the current font size.

Returns:

  • int: Current font size

Example:

# Get current font size
size = gw.font_size
print(f"Current font size: {size}")

set_font_size

set_font_size(size: int) -> 'Gw'

Set the font size.

Parameters:

  • size (int): Sets the font size

Returns:

  • Gw: Self for method chaining

font_name

font_name -> str

Property that returns the current font name.

Returns:

  • str: Current font name

Example:

# Get current font name
font = gw.font_name
print(f"Current font: {font}")

set_font_name

set_font_name(name: str) -> 'Gw'

Set the font name.

Parameters:

  • name (str): Sets the font name

Returns:

  • Gw: Self for method chaining

set_image_number

set_image_number(x: int, y: int) -> 'Gw'

Set the grid dimensions for image view when using tiled display.

Parameters:

  • x (int): Number of columns in the grid
  • y (int): Number of rows in the grid

Returns:

  • Gw: Self for method chaining

Example:

# Set up a 2x3 grid layout
gw.set_image_number(2, 3)

__ array_interface __

The Gw object implements the NumPy array interface protocol, allowing it to be directly converted to a NumPy array without copying the underlying data.

Returns:

  • dict or None: Describes the underlying image buffer if the raster surface exists, otherwise None

Example:

import numpy as np

# Convert to numpy array with zero-copy
gw.draw()  # Ensure the image is rendered
arr = np.asarray(gw)  # Uses __array_interface__ automatically

Configuration Properties

gwplot provides numerous properties that can be accessed or modified to configure the visualisation:

Thread and Memory Settings

  • threads / set_threads(num: int) -> 'Gw': Get/set the number of processing threads
  • low_memory / set_low_memory(size: int) -> 'Gw': Get/set low memory mode threshold in base-pairs

Visualisation Parameters

  • indel_length / set_indel_length(length: int) -> 'Gw': Get/set indel length threshold for labeling
  • ylim / set_ylim(limit: int) -> 'Gw': Get/set the y-axis limit
  • split_view_size / set_split_view_size(size: int) -> 'Gw': Get/set the split view size
  • pad / set_pad(padding: int) -> 'Gw': Get/set the padding between elements
  • max_coverage / set_max_coverage(coverage: int) -> 'Gw': Get/set maximum coverage value
  • max_tlen / set_max_tlen(length: int) -> 'Gw': Get/set maximum template length
  • log2_cov / set_log2_cov(enabled: bool) -> 'Gw': Get/set log2 coverage display
  • tlen_yscale / set_tlen_yscale(scale: bool) -> 'Gw': Get/set template length y-scale
  • expand_tracks / set_expand_tracks(expand: bool) -> 'Gw': Get/set track expansion
  • vcf_as_tracks / set_vcf_as_tracks(as_tracks: bool) -> 'Gw': Get/set VCF display as tracks
  • sv_arcs / set_sv_arcs(arcs: bool) -> 'Gw': Get/set structural variant arcs display
  • scroll_speed / set_scroll_speed(speed: float) -> 'Gw': Get/set the scroll speed
  • tab_track_height / set_tab_track_height(height: float) -> 'Gw': Get/set track tab height
  • start_index / set_start_index(index: int) -> 'Gw': Get/set coordinate start index (0 or 1)
  • soft_clip_threshold / set_soft_clip_threshold(threshold: int) -> 'Gw': Get/set soft clip threshold
  • small_indel_threshold / set_small_indel_threshold(threshold: int) -> 'Gw': Get/set small indel threshold
  • snp_threshold / set_snp_threshold(threshold: int) -> 'Gw': Get/set SNP threshold
  • variant_distance / set_variant_distance(distance: int) -> 'Gw': Get/set variant distance threshold