Draw an A3 Amino Acid Sequence Visualization

Renders an A3 object (from rtemis.a3) as an interactive ECharts amino-acid sequence diagram. The sequence is wrapped into rows in a meander/serpentine path, with optional site, region, PTM, processing, and variant annotations overlaid as distinct series and collected in a vertical legend.

Usage

draw_a3(
  x,
  n_per_row = 21L,
  residue_spacing = 0.3,
  marker_size = 28,
  font_size = 18,
  line_width = 2,
  show_markers = TRUE,
  show_labels = TRUE,
  position_every = 10L,
  region_opacity = 0.35,
  ptm_placement = "radial",
  residue_fill = "#E7E5E4",
  residue_stroke = "#44403C",
  label_color = "#1C1917",
  pos_label_color = "#78716C",
  variant_color = "#FA6E1E",
  disease_variant_color = "#E266AE",
  enable_zoom = TRUE,
  title = NULL,
  grid = NULL,
  theme = NULL,
  width = NULL,
  height = NULL,
  filename = NULL
)

Arguments

x: A3 object from rtemis.a3::create_A3() or rtemis.a3::read_A3json().
n_per_row: Integer [2, Inf): Number of residues per wrapped row.
residue_spacing: Numeric (0, Inf): Horizontal spacing multiplier. Values below 1 compress the layout; 1 gives natural hex spacing.
marker_size: Numeric (0, Inf): Residue circle diameter in pixels.
font_size: Numeric (0, Inf): Base font size in pixels for residue and position labels.
line_width: Numeric (0, Inf): Backbone line width in pixels.
show_markers: Logical: Whether to render the backbone line and residue circles.
show_labels: Logical: Whether to render single-letter residue labels.
position_every: Optional Integer [1, Inf): Show a numeric position label every N residues. NULL disables position labels.
region_opacity: Numeric [0, 1]: Opacity of region band overlays.
ptm_placement: Character {"radial", "innerRadial", "outerRadial"}: Placement of PTM symbols relative to the residue circle. "radial" centres on the circle edge; "innerRadial" places inside; "outerRadial" places outside.
residue_fill: Character: Residue circle fill color.
residue_stroke: Character: Residue circle stroke and backbone line color.
label_color: Character: Default residue label text color.
pos_label_color: Character: Position label text color.
variant_color: Character: Label color for variant residues.
disease_variant_color: Character: Label color for disease-associated variant residues (takes precedence over variant_color).
enable_zoom: Logical: Whether to enable Shift+scroll zoom.
title: Optional Character: Chart title.
grid: Optional Grid: Override any plot-area margin. The defaults (left = 24, top auto, right driven by legend width, bottom = 24) are merged with the properties of the supplied Grid object, so only the fields you set are changed — e.g. Grid(left = 8, top = 8). legend_top is re-derived from the final grid top automatically.
theme: Optional Theme: Theme override. NULL auto-detects light/dark mode; NA uses raw ECharts defaults.
width: Optional Numeric or Character: Widget width.
height: Optional Numeric or Character: Widget height. Auto-computed from layout bounds and marker_size when NULL.
filename: Optional Character: If provided, save the widget to this file via save_drawing().

Value

htmlwidget: Widget object.

Details

Corresponds to createA3EChartsOption() in src/lib/a3/visualization/echarts.ts.

Examples

if (requireNamespace("rtemis.a3", quietly = TRUE)) {
  a <- rtemis.a3::create_A3(
    "MAEPRQEFEVMEDHAGTYGLGDRK",
    site = list(
      Active_site = rtemis.a3::annotation_position(c(5L, 17L))
    ),
    region = list(
      Domain = rtemis.a3::annotation_range(
        matrix(c(3L, 10L, 15L, 22L), ncol = 2, byrow = TRUE)
      )
    )
  )
  draw_a3(a)
}